Starting phenix.real_space_refine on Sun Apr 27 05:02:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fnb_50587/04_2025/9fnb_50587_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fnb_50587/04_2025/9fnb_50587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fnb_50587/04_2025/9fnb_50587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fnb_50587/04_2025/9fnb_50587.map" model { file = "/net/cci-nas-00/data/ceres_data/9fnb_50587/04_2025/9fnb_50587_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fnb_50587/04_2025/9fnb_50587_neut.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 28 5.16 5 C 2904 2.51 5 N 708 2.21 5 O 928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4568 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: C, B, D Time building chain proxies: 3.61, per 1000 atoms: 0.79 Number of scatterers: 4568 At special positions: 0 Unit cell: (102.176, 104.648, 37.08, 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 28 16.00 O 928 8.00 N 708 7.00 C 2904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 301 " - " ASN A 145 " " NAG A 302 " - " ASN A 151 " " NAG A 303 " - " ASN A 164 " " NAG B 301 " - " ASN B 145 " " NAG B 302 " - " ASN B 151 " " NAG B 303 " - " ASN B 164 " " NAG C 301 " - " ASN C 145 " " NAG C 302 " - " ASN C 151 " " NAG C 303 " - " ASN C 164 " " NAG D 301 " - " ASN D 145 " " NAG D 302 " - " ASN D 151 " " NAG D 303 " - " ASN D 164 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 550.4 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 74.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 126 removed outlier: 6.961A pdb=" N ASP A 122 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE B 121 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N LYS C 124 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL B 123 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE C 126 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR B 125 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASP B 122 " --> pdb=" O ILE D 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 removed outlier: 6.659A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.817A pdb=" N VAL A 133 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 133 " --> pdb=" O SER D 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 176 removed outlier: 7.046A pdb=" N ILE A 142 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR C 143 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU A 144 " --> pdb=" O TYR C 143 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN C 145 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 162 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLU C 163 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASN A 164 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE C 165 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR A 166 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N THR B 141 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N LEU C 144 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N TYR B 143 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N ILE C 146 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN B 145 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ASN C 148 " --> pdb=" O ASN B 145 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR B 147 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU C 150 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR B 149 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE C 152 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN B 151 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASN C 154 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR B 153 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASN C 156 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN B 155 " --> pdb=" O ASN C 156 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N TYR C 158 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR B 157 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL C 160 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER B 159 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL C 162 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLU B 161 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 9.933A pdb=" N ASN C 164 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N GLU B 163 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N THR C 166 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE B 165 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN C 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA B 167 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLN C 170 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL B 169 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N SER C 172 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE B 171 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR C 174 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS B 173 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ILE C 176 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 175 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE B 142 " --> pdb=" O THR D 141 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TYR D 143 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU B 144 " --> pdb=" O TYR D 143 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN D 145 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 162 " --> pdb=" O GLU D 161 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLU D 163 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASN B 164 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE D 165 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR B 166 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 187 removed outlier: 6.953A pdb=" N ILE C 184 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR A 185 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE C 186 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE A 187 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG B 180 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ASN C 183 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N ASN B 182 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N THR C 185 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N ILE B 184 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N ILE C 187 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N ILE B 186 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE D 184 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR B 185 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE D 186 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE B 187 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 191 through 198 removed outlier: 6.898A pdb=" N ILE C 195 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP A 196 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR C 197 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A 198 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP B 191 " --> pdb=" O MET C 192 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N GLN C 194 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N LYS B 193 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ASP C 196 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N ILE B 195 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 10.374A pdb=" N THR C 198 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N TYR B 197 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE D 195 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP B 196 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR D 197 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR B 198 " --> pdb=" O TYR D 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 206 removed outlier: 6.458A pdb=" N THR A 201 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA C 204 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE A 203 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLU C 206 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU A 205 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR B 201 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA D 204 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 203 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLU D 206 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU B 205 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 209 through 230 removed outlier: 9.190A pdb=" N TYR A 209 " --> pdb=" O MET C 210 " (cutoff:3.500A) removed outlier: 10.599A pdb=" N ASP C 212 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N TYR A 211 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N CYS C 214 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A 213 " --> pdb=" O CYS C 214 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N LEU C 216 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR A 215 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N SER C 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 217 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N LYS C 220 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE A 219 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N HIS C 222 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N VAL A 221 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N ILE C 224 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN A 223 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU C 226 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL A 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N MET C 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N MET A 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL C 230 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLN A 229 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N MET B 210 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N TYR C 211 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP B 212 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE C 213 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N CYS B 214 " --> pdb=" O PHE C 213 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL C 221 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N HIS B 222 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN C 223 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 230 " --> pdb=" O GLN C 229 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N TYR B 209 " --> pdb=" O MET D 210 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N ASP D 212 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N TYR B 211 " --> pdb=" O ASP D 212 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N CYS D 214 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE B 213 " --> pdb=" O CYS D 214 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N LEU D 216 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR B 215 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N SER D 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE B 217 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N LYS D 220 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE B 219 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N HIS D 222 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N VAL B 221 " --> pdb=" O HIS D 222 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N ILE D 224 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASN B 223 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU D 226 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL B 225 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N MET D 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N MET B 227 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL D 230 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLN B 229 " --> pdb=" O VAL D 230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 233 through 252 removed outlier: 6.548A pdb=" N THR A 233 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N TYR C 236 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR A 235 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLY C 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N PHE A 237 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N SER C 240 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS A 239 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N GLN C 242 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU A 241 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N SER C 244 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 243 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLU C 246 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN A 245 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N TYR C 248 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG A 247 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N TYR C 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N GLN A 249 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASP C 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N VAL A 251 " --> pdb=" O ASP C 252 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL C 251 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP B 252 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR B 233 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N TYR D 236 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR B 235 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N GLY D 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N PHE B 237 " --> pdb=" O GLY D 238 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N SER D 240 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N HIS B 239 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N GLN D 242 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU B 241 " --> pdb=" O GLN D 242 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N SER D 244 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE B 243 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLU D 246 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN B 245 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N TYR D 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG B 247 " --> pdb=" O TYR D 248 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N TYR D 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N GLN B 249 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASP D 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N VAL B 251 " --> pdb=" O ASP D 252 " (cutoff:3.500A) 109 hydrogen bonds defined for protein. 327 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: 1.12 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1137 1.34 - 1.46: 1377 1.46 - 1.58: 2078 1.58 - 1.70: 0 1.70 - 1.83: 48 Bond restraints: 4640 Sorted by residual: bond pdb=" CG HIS C 222 " pdb=" CD2 HIS C 222 " ideal model delta sigma weight residual 1.354 1.329 0.025 1.10e-02 8.26e+03 5.13e+00 bond pdb=" CA ALA C 167 " pdb=" CB ALA C 167 " ideal model delta sigma weight residual 1.532 1.491 0.040 1.82e-02 3.02e+03 4.95e+00 bond pdb=" CG HIS D 222 " pdb=" CD2 HIS D 222 " ideal model delta sigma weight residual 1.354 1.330 0.024 1.10e-02 8.26e+03 4.84e+00 bond pdb=" CG HIS B 222 " pdb=" CD2 HIS B 222 " ideal model delta sigma weight residual 1.354 1.330 0.024 1.10e-02 8.26e+03 4.81e+00 bond pdb=" CA ALA D 167 " pdb=" CB ALA D 167 " ideal model delta sigma weight residual 1.532 1.492 0.040 1.82e-02 3.02e+03 4.78e+00 ... (remaining 4635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 4936 1.43 - 2.86: 1122 2.86 - 4.29: 176 4.29 - 5.71: 54 5.71 - 7.14: 20 Bond angle restraints: 6308 Sorted by residual: angle pdb=" N ASN A 151 " pdb=" CA ASN A 151 " pdb=" CB ASN A 151 " ideal model delta sigma weight residual 110.87 103.73 7.14 1.63e+00 3.76e-01 1.92e+01 angle pdb=" N ASN B 151 " pdb=" CA ASN B 151 " pdb=" CB ASN B 151 " ideal model delta sigma weight residual 110.87 103.74 7.13 1.63e+00 3.76e-01 1.91e+01 angle pdb=" N ASN C 151 " pdb=" CA ASN C 151 " pdb=" CB ASN C 151 " ideal model delta sigma weight residual 110.87 103.75 7.12 1.63e+00 3.76e-01 1.91e+01 angle pdb=" N ASN D 151 " pdb=" CA ASN D 151 " pdb=" CB ASN D 151 " ideal model delta sigma weight residual 110.87 103.76 7.11 1.63e+00 3.76e-01 1.90e+01 angle pdb=" N GLU B 246 " pdb=" CA GLU B 246 " pdb=" C GLU B 246 " ideal model delta sigma weight residual 108.79 114.65 -5.86 1.53e+00 4.27e-01 1.47e+01 ... (remaining 6303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.98: 2513 12.98 - 25.97: 338 25.97 - 38.95: 72 38.95 - 51.93: 20 51.93 - 64.91: 44 Dihedral angle restraints: 2987 sinusoidal: 1363 harmonic: 1624 Sorted by residual: dihedral pdb=" CA THR C 234 " pdb=" C THR C 234 " pdb=" N THR C 235 " pdb=" CA THR C 235 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR B 234 " pdb=" C THR B 234 " pdb=" N THR B 235 " pdb=" CA THR B 235 " ideal model delta harmonic sigma weight residual 180.00 158.40 21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR D 234 " pdb=" C THR D 234 " pdb=" N THR D 235 " pdb=" CA THR D 235 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 2984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 788 0.253 - 0.507: 0 0.507 - 0.760: 0 0.760 - 1.014: 4 1.014 - 1.267: 8 Chirality restraints: 800 Sorted by residual: chirality pdb=" C1 NAG D 303 " pdb=" ND2 ASN D 164 " pdb=" C2 NAG D 303 " pdb=" O5 NAG D 303 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-01 2.50e+01 4.01e+01 chirality pdb=" C1 NAG C 303 " pdb=" ND2 ASN C 164 " pdb=" C2 NAG C 303 " pdb=" O5 NAG C 303 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-01 2.50e+01 4.01e+01 chirality pdb=" C1 NAG B 303 " pdb=" ND2 ASN B 164 " pdb=" C2 NAG B 303 " pdb=" O5 NAG B 303 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-01 2.50e+01 4.01e+01 ... (remaining 797 not shown) Planarity restraints: 772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 301 " 0.052 2.00e-02 2.50e+03 4.32e-02 2.33e+01 pdb=" C7 NAG D 301 " -0.009 2.00e-02 2.50e+03 pdb=" C8 NAG D 301 " 0.038 2.00e-02 2.50e+03 pdb=" N2 NAG D 301 " -0.070 2.00e-02 2.50e+03 pdb=" O7 NAG D 301 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 301 " 0.052 2.00e-02 2.50e+03 4.30e-02 2.31e+01 pdb=" C7 NAG C 301 " -0.009 2.00e-02 2.50e+03 pdb=" C8 NAG C 301 " 0.038 2.00e-02 2.50e+03 pdb=" N2 NAG C 301 " -0.070 2.00e-02 2.50e+03 pdb=" O7 NAG C 301 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 301 " 0.052 2.00e-02 2.50e+03 4.29e-02 2.30e+01 pdb=" C7 NAG B 301 " -0.009 2.00e-02 2.50e+03 pdb=" C8 NAG B 301 " 0.038 2.00e-02 2.50e+03 pdb=" N2 NAG B 301 " -0.070 2.00e-02 2.50e+03 pdb=" O7 NAG B 301 " -0.011 2.00e-02 2.50e+03 ... (remaining 769 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 19 2.61 - 3.19: 3632 3.19 - 3.76: 6706 3.76 - 4.33: 9652 4.33 - 4.90: 17668 Nonbonded interactions: 37677 Sorted by model distance: nonbonded pdb=" SG CYS D 214 " pdb=" SG CYS D 253 " model vdw 2.042 3.760 nonbonded pdb=" SG CYS A 214 " pdb=" SG CYS A 253 " model vdw 2.042 3.760 nonbonded pdb=" SG CYS C 214 " pdb=" SG CYS C 253 " model vdw 2.043 3.760 nonbonded pdb=" OG1 THR D 231 " pdb=" OG1 THR D 234 " model vdw 2.312 3.040 nonbonded pdb=" OG1 THR A 231 " pdb=" OG1 THR A 234 " model vdw 2.312 3.040 ... (remaining 37672 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.750 Find NCS groups from input model: 0.090 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 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 : 0.009 0.094 4653 Z= 0.544 Angle : 1.408 12.087 6346 Z= 0.820 Chirality : 0.161 1.267 800 Planarity : 0.009 0.043 760 Dihedral : 15.189 64.911 1944 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.79 % Allowed : 7.94 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.32), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 222 PHE 0.019 0.006 PHE B 237 TYR 0.028 0.007 TYR D 248 ARG 0.005 0.002 ARG A 247 Details of bonding type rmsd link_NAG-ASN : bond 0.07426 ( 12) link_NAG-ASN : angle 5.91166 ( 36) hydrogen bonds : bond 0.16750 ( 109) hydrogen bonds : angle 8.12044 ( 327) SS BOND : bond 0.01130 ( 1) SS BOND : angle 2.83841 ( 2) covalent geometry : bond 0.00828 ( 4640) covalent geometry : angle 1.33889 ( 6308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8370 (mm-40) REVERT: B 192 MET cc_start: 0.8646 (mtp) cc_final: 0.8418 (mtm) REVERT: D 180 ARG cc_start: 0.8461 (mmt-90) cc_final: 0.8253 (mpt180) REVERT: D 192 MET cc_start: 0.8895 (mtp) cc_final: 0.8675 (mtm) REVERT: D 206 GLU cc_start: 0.8820 (tt0) cc_final: 0.8610 (tt0) REVERT: D 207 MET cc_start: 0.9091 (mtp) cc_final: 0.8870 (mtp) REVERT: D 228 MET cc_start: 0.9275 (ttm) cc_final: 0.9043 (ttm) outliers start: 4 outliers final: 0 residues processed: 118 average time/residue: 1.5145 time to fit residues: 183.7583 Evaluate side-chains 108 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 0.0570 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN A 138 GLN A 229 GLN C 229 GLN D 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.109579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088601 restraints weight = 5247.489| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.00 r_work: 0.3237 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4653 Z= 0.159 Angle : 0.601 4.905 6346 Z= 0.326 Chirality : 0.051 0.130 800 Planarity : 0.003 0.019 760 Dihedral : 6.841 42.887 932 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.39 % Allowed : 11.90 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.33), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 239 PHE 0.011 0.002 PHE C 237 TYR 0.017 0.002 TYR A 143 ARG 0.002 0.000 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00091 ( 12) link_NAG-ASN : angle 1.59238 ( 36) hydrogen bonds : bond 0.02797 ( 109) hydrogen bonds : angle 6.07190 ( 327) SS BOND : bond 0.00567 ( 1) SS BOND : angle 0.65749 ( 2) covalent geometry : bond 0.00370 ( 4640) covalent geometry : angle 0.59100 ( 6308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 MET cc_start: 0.8359 (mtp) cc_final: 0.8046 (mtm) REVERT: B 207 MET cc_start: 0.8779 (mtp) cc_final: 0.8552 (mtm) REVERT: C 206 GLU cc_start: 0.8395 (tt0) cc_final: 0.8189 (tt0) REVERT: D 124 LYS cc_start: 0.9259 (mttt) cc_final: 0.8991 (mttm) REVERT: D 139 LYS cc_start: 0.8128 (ttmt) cc_final: 0.6981 (mmpt) REVERT: D 192 MET cc_start: 0.8655 (mtp) cc_final: 0.8377 (mtm) REVERT: D 207 MET cc_start: 0.8999 (mtp) cc_final: 0.8649 (mtp) REVERT: D 228 MET cc_start: 0.9296 (ttm) cc_final: 0.9031 (ttm) outliers start: 7 outliers final: 0 residues processed: 113 average time/residue: 1.5146 time to fit residues: 176.0422 Evaluate side-chains 110 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN B 194 GLN A 138 GLN A 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.107931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.086938 restraints weight = 5268.090| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.01 r_work: 0.3216 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4653 Z= 0.206 Angle : 0.635 5.138 6346 Z= 0.342 Chirality : 0.051 0.132 800 Planarity : 0.003 0.024 760 Dihedral : 6.589 28.182 932 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.59 % Allowed : 12.70 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.32), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 239 PHE 0.013 0.003 PHE D 171 TYR 0.017 0.002 TYR C 143 ARG 0.001 0.000 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00105 ( 12) link_NAG-ASN : angle 1.66671 ( 36) hydrogen bonds : bond 0.03077 ( 109) hydrogen bonds : angle 5.90652 ( 327) SS BOND : bond 0.00510 ( 1) SS BOND : angle 0.67625 ( 2) covalent geometry : bond 0.00485 ( 4640) covalent geometry : angle 0.62440 ( 6308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8177 (mtpt) REVERT: B 192 MET cc_start: 0.8392 (mtp) cc_final: 0.8072 (mtm) REVERT: B 207 MET cc_start: 0.8757 (mtp) cc_final: 0.8520 (mtm) REVERT: C 206 GLU cc_start: 0.8446 (tt0) cc_final: 0.8229 (tt0) REVERT: D 124 LYS cc_start: 0.9283 (mttt) cc_final: 0.9051 (mttm) REVERT: D 139 LYS cc_start: 0.8227 (ttmt) cc_final: 0.6903 (tppt) REVERT: D 192 MET cc_start: 0.8684 (mtp) cc_final: 0.8381 (mtm) REVERT: D 207 MET cc_start: 0.9037 (mtp) cc_final: 0.8685 (mtp) REVERT: D 209 TYR cc_start: 0.7950 (m-80) cc_final: 0.7742 (m-80) REVERT: D 228 MET cc_start: 0.9290 (ttm) cc_final: 0.9026 (ttm) outliers start: 8 outliers final: 0 residues processed: 119 average time/residue: 1.5432 time to fit residues: 188.6831 Evaluate side-chains 114 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN B 194 GLN A 138 GLN A 229 GLN C 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.106417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.085689 restraints weight = 5347.584| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.01 r_work: 0.3198 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 4653 Z= 0.258 Angle : 0.677 6.551 6346 Z= 0.362 Chirality : 0.052 0.132 800 Planarity : 0.003 0.028 760 Dihedral : 7.153 37.439 932 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.79 % Allowed : 13.49 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.32), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 239 PHE 0.014 0.003 PHE B 213 TYR 0.018 0.002 TYR B 143 ARG 0.001 0.000 ARG C 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 12) link_NAG-ASN : angle 1.81380 ( 36) hydrogen bonds : bond 0.03223 ( 109) hydrogen bonds : angle 5.91178 ( 327) SS BOND : bond 0.00663 ( 1) SS BOND : angle 0.73601 ( 2) covalent geometry : bond 0.00609 ( 4640) covalent geometry : angle 0.66481 ( 6308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 LYS cc_start: 0.8468 (mtpt) cc_final: 0.8161 (mtpt) REVERT: B 192 MET cc_start: 0.8384 (mtp) cc_final: 0.8039 (mtm) REVERT: B 207 MET cc_start: 0.8775 (mtp) cc_final: 0.8514 (mtm) REVERT: D 139 LYS cc_start: 0.8350 (ttmt) cc_final: 0.6875 (tppt) REVERT: D 192 MET cc_start: 0.8684 (mtp) cc_final: 0.8375 (mtm) REVERT: D 209 TYR cc_start: 0.7966 (m-80) cc_final: 0.7631 (m-80) outliers start: 9 outliers final: 1 residues processed: 119 average time/residue: 1.5758 time to fit residues: 192.6390 Evaluate side-chains 117 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 249 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN B 194 GLN B 229 GLN A 138 GLN A 229 GLN C 138 GLN C 229 GLN D 229 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.106776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.086089 restraints weight = 5384.625| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.02 r_work: 0.3209 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4653 Z= 0.208 Angle : 0.643 8.019 6346 Z= 0.342 Chirality : 0.051 0.129 800 Planarity : 0.003 0.020 760 Dihedral : 6.762 28.397 932 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.39 % Allowed : 15.08 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.32), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.013 0.003 PHE D 171 TYR 0.016 0.002 TYR A 143 ARG 0.001 0.000 ARG C 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00114 ( 12) link_NAG-ASN : angle 1.78604 ( 36) hydrogen bonds : bond 0.02908 ( 109) hydrogen bonds : angle 5.73928 ( 327) SS BOND : bond 0.00554 ( 1) SS BOND : angle 0.61736 ( 2) covalent geometry : bond 0.00490 ( 4640) covalent geometry : angle 0.63039 ( 6308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 LEU cc_start: 0.8900 (tt) cc_final: 0.8688 (tt) REVERT: B 178 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8203 (mtpt) REVERT: B 192 MET cc_start: 0.8382 (mtp) cc_final: 0.8055 (mtm) REVERT: D 139 LYS cc_start: 0.8300 (ttmt) cc_final: 0.6890 (tppt) REVERT: D 192 MET cc_start: 0.8613 (mtp) cc_final: 0.8297 (mtm) REVERT: D 209 TYR cc_start: 0.8014 (m-80) cc_final: 0.7640 (m-80) outliers start: 7 outliers final: 0 residues processed: 117 average time/residue: 1.6154 time to fit residues: 194.0639 Evaluate side-chains 114 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN B 194 GLN A 138 GLN A 229 GLN C 138 GLN C 229 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.108545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.087721 restraints weight = 5305.727| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.01 r_work: 0.3238 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4653 Z= 0.163 Angle : 0.609 8.951 6346 Z= 0.323 Chirality : 0.051 0.128 800 Planarity : 0.002 0.019 760 Dihedral : 6.334 26.900 932 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.19 % Allowed : 16.27 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.32), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 239 PHE 0.012 0.003 PHE D 171 TYR 0.015 0.002 TYR A 143 ARG 0.001 0.000 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 12) link_NAG-ASN : angle 1.72063 ( 36) hydrogen bonds : bond 0.02590 ( 109) hydrogen bonds : angle 5.59658 ( 327) SS BOND : bond 0.00483 ( 1) SS BOND : angle 0.54137 ( 2) covalent geometry : bond 0.00382 ( 4640) covalent geometry : angle 0.59661 ( 6308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 LYS cc_start: 0.8437 (mtpt) cc_final: 0.8136 (mtpt) REVERT: B 192 MET cc_start: 0.8393 (mtp) cc_final: 0.8060 (mtm) REVERT: C 138 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8456 (mm-40) REVERT: C 192 MET cc_start: 0.8518 (mtp) cc_final: 0.8310 (mtm) REVERT: D 139 LYS cc_start: 0.8235 (ttmt) cc_final: 0.6891 (tppt) REVERT: D 192 MET cc_start: 0.8651 (mtp) cc_final: 0.8330 (mtm) REVERT: D 209 TYR cc_start: 0.7977 (m-80) cc_final: 0.7681 (m-80) outliers start: 6 outliers final: 1 residues processed: 116 average time/residue: 1.6342 time to fit residues: 194.6960 Evaluate side-chains 113 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 249 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN B 194 GLN A 138 GLN A 229 GLN C 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.105025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.084561 restraints weight = 5406.613| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.00 r_work: 0.3187 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 4653 Z= 0.315 Angle : 0.729 10.279 6346 Z= 0.385 Chirality : 0.053 0.133 800 Planarity : 0.004 0.037 760 Dihedral : 7.360 38.549 932 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.59 % Allowed : 15.67 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.32), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.014 0.003 PHE D 171 TYR 0.019 0.003 TYR C 135 ARG 0.002 0.000 ARG D 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 12) link_NAG-ASN : angle 1.86884 ( 36) hydrogen bonds : bond 0.03461 ( 109) hydrogen bonds : angle 5.87895 ( 327) SS BOND : bond 0.00633 ( 1) SS BOND : angle 0.70926 ( 2) covalent geometry : bond 0.00744 ( 4640) covalent geometry : angle 0.71736 ( 6308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8211 (mtpt) REVERT: B 192 MET cc_start: 0.8373 (mtp) cc_final: 0.8014 (mtm) REVERT: A 228 MET cc_start: 0.9423 (ttm) cc_final: 0.9210 (ttm) REVERT: D 139 LYS cc_start: 0.8351 (ttmt) cc_final: 0.6878 (tppt) REVERT: D 178 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8156 (mtpp) REVERT: D 192 MET cc_start: 0.8678 (mtp) cc_final: 0.8387 (mtm) REVERT: D 209 TYR cc_start: 0.8044 (m-80) cc_final: 0.7601 (m-80) outliers start: 8 outliers final: 0 residues processed: 123 average time/residue: 1.6529 time to fit residues: 208.8113 Evaluate side-chains 120 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN B 182 ASN B 183 ASN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN A 182 ASN A 183 ASN A 229 GLN C 182 ASN C 183 ASN D 194 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.092629 restraints weight = 5190.312| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.01 r_work: 0.3323 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 4653 Z= 0.088 Angle : 0.551 11.084 6346 Z= 0.290 Chirality : 0.050 0.132 800 Planarity : 0.002 0.020 760 Dihedral : 5.733 30.744 932 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.60 % Allowed : 17.26 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.32), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.011 0.002 PHE D 171 TYR 0.012 0.001 TYR B 248 ARG 0.002 0.000 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00123 ( 12) link_NAG-ASN : angle 1.61072 ( 36) hydrogen bonds : bond 0.01990 ( 109) hydrogen bonds : angle 5.32451 ( 327) SS BOND : bond 0.00306 ( 1) SS BOND : angle 0.45975 ( 2) covalent geometry : bond 0.00189 ( 4640) covalent geometry : angle 0.53934 ( 6308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7877 (mm-40) REVERT: B 178 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8126 (mtpt) REVERT: B 192 MET cc_start: 0.8370 (mtp) cc_final: 0.8033 (mtm) REVERT: C 138 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8411 (mm-40) REVERT: D 139 LYS cc_start: 0.8010 (ttmt) cc_final: 0.6757 (tppt) REVERT: D 140 ARG cc_start: 0.7294 (tpt170) cc_final: 0.7014 (tpt170) REVERT: D 192 MET cc_start: 0.8607 (mtp) cc_final: 0.8301 (mtm) REVERT: D 209 TYR cc_start: 0.7804 (m-80) cc_final: 0.7499 (m-80) outliers start: 3 outliers final: 0 residues processed: 118 average time/residue: 1.5505 time to fit residues: 188.0567 Evaluate side-chains 113 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.0060 overall best weight: 4.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN A 229 GLN C 229 GLN D 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.105537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085015 restraints weight = 5420.770| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.01 r_work: 0.3196 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 4653 Z= 0.284 Angle : 0.715 11.269 6346 Z= 0.377 Chirality : 0.053 0.142 800 Planarity : 0.003 0.030 760 Dihedral : 6.835 29.514 932 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.99 % Allowed : 17.66 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.32), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 239 PHE 0.014 0.003 PHE B 213 TYR 0.019 0.002 TYR B 143 ARG 0.003 0.001 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 12) link_NAG-ASN : angle 1.78856 ( 36) hydrogen bonds : bond 0.03240 ( 109) hydrogen bonds : angle 5.71060 ( 327) SS BOND : bond 0.00574 ( 1) SS BOND : angle 0.65064 ( 2) covalent geometry : bond 0.00671 ( 4640) covalent geometry : angle 0.70399 ( 6308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8224 (mtpt) REVERT: B 192 MET cc_start: 0.8392 (mtp) cc_final: 0.8040 (mtm) REVERT: B 193 LYS cc_start: 0.8636 (tttp) cc_final: 0.8415 (tptt) REVERT: A 228 MET cc_start: 0.9420 (ttm) cc_final: 0.9195 (ttm) REVERT: D 139 LYS cc_start: 0.8293 (ttmt) cc_final: 0.6897 (tppt) REVERT: D 140 ARG cc_start: 0.7420 (tpt170) cc_final: 0.7135 (tpt170) REVERT: D 178 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8153 (mtpp) REVERT: D 192 MET cc_start: 0.8650 (mtp) cc_final: 0.8354 (mtm) REVERT: D 209 TYR cc_start: 0.8028 (m-80) cc_final: 0.7575 (m-80) outliers start: 5 outliers final: 0 residues processed: 117 average time/residue: 1.6599 time to fit residues: 199.5932 Evaluate side-chains 116 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 49 optimal weight: 0.0470 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN A 229 GLN C 138 GLN C 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.108427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.087648 restraints weight = 5280.958| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.02 r_work: 0.3237 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4653 Z= 0.167 Angle : 0.636 11.152 6346 Z= 0.336 Chirality : 0.051 0.145 800 Planarity : 0.003 0.020 760 Dihedral : 6.453 29.124 932 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.60 % Allowed : 17.86 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.32), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 239 PHE 0.012 0.003 PHE C 237 TYR 0.015 0.002 TYR B 143 ARG 0.002 0.000 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 12) link_NAG-ASN : angle 1.68228 ( 36) hydrogen bonds : bond 0.02581 ( 109) hydrogen bonds : angle 5.53920 ( 327) SS BOND : bond 0.00464 ( 1) SS BOND : angle 0.54340 ( 2) covalent geometry : bond 0.00390 ( 4640) covalent geometry : angle 0.62506 ( 6308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8152 (mtpt) REVERT: B 192 MET cc_start: 0.8352 (mtp) cc_final: 0.8016 (mtm) REVERT: D 139 LYS cc_start: 0.8186 (ttmt) cc_final: 0.6820 (tppt) REVERT: D 140 ARG cc_start: 0.7337 (tpt170) cc_final: 0.7072 (tpt170) REVERT: D 192 MET cc_start: 0.8618 (mtp) cc_final: 0.8302 (mtm) REVERT: D 209 TYR cc_start: 0.7947 (m-80) cc_final: 0.7606 (m-80) outliers start: 3 outliers final: 0 residues processed: 114 average time/residue: 1.5109 time to fit residues: 176.9661 Evaluate side-chains 113 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN B 194 GLN A 138 GLN A 229 GLN C 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.106496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.085886 restraints weight = 5387.902| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.02 r_work: 0.3212 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 4653 Z= 0.240 Angle : 0.698 11.321 6346 Z= 0.368 Chirality : 0.052 0.139 800 Planarity : 0.003 0.025 760 Dihedral : 6.805 29.384 932 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.79 % Allowed : 18.65 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.32), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 239 PHE 0.014 0.003 PHE D 171 TYR 0.017 0.002 TYR B 143 ARG 0.002 0.000 ARG B 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 12) link_NAG-ASN : angle 1.75895 ( 36) hydrogen bonds : bond 0.03020 ( 109) hydrogen bonds : angle 5.68754 ( 327) SS BOND : bond 0.00540 ( 1) SS BOND : angle 0.62460 ( 2) covalent geometry : bond 0.00566 ( 4640) covalent geometry : angle 0.68719 ( 6308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4793.26 seconds wall clock time: 82 minutes 20.48 seconds (4940.48 seconds total)