Starting phenix.real_space_refine on Thu Mar 6 02:52:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fnb_50587/03_2025/9fnb_50587_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fnb_50587/03_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_50587/03_2025/9fnb_50587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fnb_50587/03_2025/9fnb_50587.map" model { file = "/net/cci-nas-00/data/ceres_data/9fnb_50587/03_2025/9fnb_50587_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fnb_50587/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.90, per 1000 atoms: 0.85 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: 1.09 Conformation dependent library (CDL) restraints added in 538.6 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: 0.45 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: 1.03 Time building geometry restraints manager: 1.31 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: 0.03 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: 3.820 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: 15.060 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.280 ------------------------------------------------------------------------------- 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 : 0.008 0.047 4640 Z= 0.529 Angle : 1.339 7.142 6308 Z= 0.808 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 *********************** 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 : 0.512 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: 1.6290 time to fit residues: 197.3678 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 : 0.551 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.0060 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 0.0570 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.4120 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.112811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.091414 restraints weight = 5185.429| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.04 r_work: 0.3277 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4640 Z= 0.159 Angle : 0.541 4.303 6308 Z= 0.299 Chirality : 0.050 0.135 800 Planarity : 0.002 0.014 760 Dihedral : 6.762 45.946 932 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.59 % Allowed : 11.71 % 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: -2.32 (0.33), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 239 PHE 0.010 0.002 PHE C 237 TYR 0.015 0.002 TYR A 143 ARG 0.001 0.000 ARG B 180 *********************** 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 124 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 MET cc_start: 0.8356 (mtp) cc_final: 0.8068 (mtm) REVERT: B 207 MET cc_start: 0.8786 (mtp) cc_final: 0.8559 (mtm) REVERT: C 124 LYS cc_start: 0.9164 (mttt) cc_final: 0.8920 (mttm) REVERT: D 124 LYS cc_start: 0.9186 (mttt) cc_final: 0.8923 (mttm) REVERT: D 139 LYS cc_start: 0.8051 (ttmt) cc_final: 0.6993 (mmpt) REVERT: D 192 MET cc_start: 0.8650 (mtp) cc_final: 0.8362 (mtm) REVERT: D 207 MET cc_start: 0.8964 (mtp) cc_final: 0.8617 (mtp) outliers start: 8 outliers final: 0 residues processed: 118 average time/residue: 1.5354 time to fit residues: 186.3229 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 : 0.486 ------------------------------------------------------------------------------- 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: 7.9990 chunk 28 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 46 optimal weight: 0.0970 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN B 229 GLN A 138 GLN A 229 GLN C 229 GLN D 229 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.109674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.088555 restraints weight = 5225.641| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.01 r_work: 0.3244 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4640 Z= 0.238 Angle : 0.580 5.152 6308 Z= 0.318 Chirality : 0.051 0.129 800 Planarity : 0.002 0.016 760 Dihedral : 6.048 23.107 932 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.38 % Allowed : 12.30 % Favored : 85.32 % 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: -2.30 (0.33), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 239 PHE 0.012 0.003 PHE D 171 TYR 0.016 0.002 TYR B 143 ARG 0.001 0.000 ARG B 180 *********************** 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 126 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 MET cc_start: 0.8394 (mtp) cc_final: 0.8093 (mtm) REVERT: B 207 MET cc_start: 0.8783 (mtp) cc_final: 0.8524 (mtm) REVERT: D 124 LYS cc_start: 0.9261 (mttt) cc_final: 0.9041 (mttm) REVERT: D 139 LYS cc_start: 0.8093 (ttmt) cc_final: 0.6899 (tppt) REVERT: D 192 MET cc_start: 0.8684 (mtp) cc_final: 0.8385 (mtm) outliers start: 12 outliers final: 0 residues processed: 117 average time/residue: 1.6055 time to fit residues: 192.8517 Evaluate side-chains 112 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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: 7.9990 chunk 8 optimal weight: 7.9990 chunk 20 optimal weight: 0.0970 chunk 44 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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 D 138 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.107351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.086541 restraints weight = 5313.955| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.00 r_work: 0.3214 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4640 Z= 0.322 Angle : 0.625 6.244 6308 Z= 0.339 Chirality : 0.051 0.131 800 Planarity : 0.003 0.021 760 Dihedral : 6.610 28.367 932 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.59 % Allowed : 13.29 % Favored : 85.12 % 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 : -1.76 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.013 0.003 PHE B 213 TYR 0.016 0.002 TYR C 143 ARG 0.001 0.000 ARG B 180 *********************** 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 124 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8113 (mtpt) REVERT: B 192 MET cc_start: 0.8390 (mtp) cc_final: 0.8071 (mtm) REVERT: B 207 MET cc_start: 0.8782 (mtp) cc_final: 0.8544 (mtm) REVERT: D 139 LYS cc_start: 0.8244 (ttmt) cc_final: 0.6976 (tppt) REVERT: D 192 MET cc_start: 0.8672 (mtp) cc_final: 0.8373 (mtm) REVERT: D 207 MET cc_start: 0.9055 (mtp) cc_final: 0.8703 (mtp) REVERT: D 209 TYR cc_start: 0.7907 (m-80) cc_final: 0.7658 (m-80) outliers start: 8 outliers final: 0 residues processed: 118 average time/residue: 1.5441 time to fit residues: 187.2244 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 : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.107010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.086328 restraints weight = 5372.123| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.00 r_work: 0.3211 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4640 Z= 0.336 Angle : 0.637 8.032 6308 Z= 0.343 Chirality : 0.051 0.130 800 Planarity : 0.003 0.022 760 Dihedral : 6.720 27.255 932 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.59 % Allowed : 14.29 % Favored : 84.13 % 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: -2.30 (0.32), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (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 C 135 ARG 0.001 0.000 ARG B 180 *********************** 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 121 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 LEU cc_start: 0.8905 (tt) cc_final: 0.8681 (tt) REVERT: B 178 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8121 (mtpt) REVERT: B 192 MET cc_start: 0.8380 (mtp) cc_final: 0.8049 (mtm) REVERT: B 207 MET cc_start: 0.8778 (mtp) cc_final: 0.8482 (mtm) REVERT: D 139 LYS cc_start: 0.8253 (ttmt) cc_final: 0.6905 (tppt) REVERT: D 192 MET cc_start: 0.8647 (mtp) cc_final: 0.8352 (mtm) REVERT: D 209 TYR cc_start: 0.7897 (m-80) cc_final: 0.7606 (m-80) outliers start: 8 outliers final: 0 residues processed: 115 average time/residue: 1.5119 time to fit residues: 178.6979 Evaluate side-chains 112 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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: 7.9990 chunk 3 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 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 = 0.3644 r_free = 0.3644 target = 0.106829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.086227 restraints weight = 5340.049| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.01 r_work: 0.3211 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4640 Z= 0.318 Angle : 0.629 8.917 6308 Z= 0.338 Chirality : 0.051 0.129 800 Planarity : 0.003 0.020 760 Dihedral : 6.658 27.297 932 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.79 % Allowed : 14.88 % Favored : 83.33 % 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 0.002 HIS C 239 PHE 0.013 0.003 PHE D 171 TYR 0.015 0.002 TYR A 143 ARG 0.001 0.000 ARG B 180 *********************** 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 122 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 LYS cc_start: 0.8445 (mtpt) cc_final: 0.8142 (mtpt) REVERT: B 192 MET cc_start: 0.8364 (mtp) cc_final: 0.8044 (mtm) REVERT: D 139 LYS cc_start: 0.8280 (ttmt) cc_final: 0.6925 (tppt) REVERT: D 192 MET cc_start: 0.8619 (mtp) cc_final: 0.8304 (mtm) REVERT: D 209 TYR cc_start: 0.7939 (m-80) cc_final: 0.7636 (m-80) outliers start: 9 outliers final: 1 residues processed: 115 average time/residue: 1.4684 time to fit residues: 173.5797 Evaluate side-chains 111 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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: 7.9990 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.107704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.087035 restraints weight = 5323.076| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.00 r_work: 0.3228 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4640 Z= 0.268 Angle : 0.607 9.355 6308 Z= 0.327 Chirality : 0.051 0.127 800 Planarity : 0.003 0.019 760 Dihedral : 6.422 26.929 932 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.99 % Allowed : 15.87 % Favored : 83.13 % 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 : -1.77 (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 B 143 ARG 0.002 0.000 ARG B 180 *********************** 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 119 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 LYS cc_start: 0.9075 (mttt) cc_final: 0.8775 (mttt) REVERT: B 178 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8077 (mtpt) REVERT: B 192 MET cc_start: 0.8326 (mtp) cc_final: 0.7992 (mtm) REVERT: C 192 MET cc_start: 0.8487 (mtp) cc_final: 0.8283 (mtm) REVERT: D 139 LYS cc_start: 0.8233 (ttmt) cc_final: 0.6916 (tppt) REVERT: D 192 MET cc_start: 0.8630 (mtp) cc_final: 0.8311 (mtm) REVERT: D 209 TYR cc_start: 0.7917 (m-80) cc_final: 0.7598 (m-80) outliers start: 5 outliers final: 0 residues processed: 116 average time/residue: 1.5016 time to fit residues: 179.0422 Evaluate side-chains 112 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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: 1.9990 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 24 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 A 182 ASN A 183 ASN A 229 GLN C 182 ASN C 183 ASN C 229 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.111223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090170 restraints weight = 5236.434| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.02 r_work: 0.3274 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4640 Z= 0.173 Angle : 0.562 9.867 6308 Z= 0.301 Chirality : 0.050 0.127 800 Planarity : 0.002 0.019 760 Dihedral : 5.844 26.093 932 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.99 % Allowed : 16.87 % 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: -2.34 (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 A 239 PHE 0.011 0.002 PHE D 171 TYR 0.014 0.002 TYR A 211 ARG 0.001 0.000 ARG B 180 *********************** 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 120 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 LYS cc_start: 0.8397 (mtpt) cc_final: 0.8076 (mtpt) REVERT: B 192 MET cc_start: 0.8331 (mtp) cc_final: 0.7979 (mtm) REVERT: C 192 MET cc_start: 0.8510 (mtp) cc_final: 0.8280 (mtm) REVERT: D 139 LYS cc_start: 0.8070 (ttmt) cc_final: 0.6851 (tppt) REVERT: D 192 MET cc_start: 0.8643 (mtp) cc_final: 0.8332 (mtm) REVERT: D 207 MET cc_start: 0.9098 (mtp) cc_final: 0.8726 (mtp) REVERT: D 209 TYR cc_start: 0.7870 (m-80) cc_final: 0.7652 (m-80) outliers start: 5 outliers final: 0 residues processed: 117 average time/residue: 1.6379 time to fit residues: 196.8347 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 : 0.520 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN A 138 GLN A 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.107652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.086894 restraints weight = 5353.452| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.02 r_work: 0.3226 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4640 Z= 0.287 Angle : 0.632 10.829 6308 Z= 0.339 Chirality : 0.051 0.128 800 Planarity : 0.003 0.018 760 Dihedral : 6.400 28.392 932 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.79 % Allowed : 17.06 % 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: -2.31 (0.32), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 239 PHE 0.013 0.003 PHE D 171 TYR 0.016 0.002 TYR B 143 ARG 0.002 0.000 ARG B 180 *********************** 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 117 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8091 (mtpt) REVERT: B 192 MET cc_start: 0.8319 (mtp) cc_final: 0.7990 (mtm) REVERT: B 193 LYS cc_start: 0.8605 (tttp) cc_final: 0.8348 (tptt) REVERT: C 192 MET cc_start: 0.8499 (mtp) cc_final: 0.8268 (mtm) REVERT: D 139 LYS cc_start: 0.8149 (ttmt) cc_final: 0.6908 (tppt) REVERT: D 192 MET cc_start: 0.8641 (mtp) cc_final: 0.8329 (mtm) REVERT: D 209 TYR cc_start: 0.7948 (m-80) cc_final: 0.7660 (m-80) outliers start: 4 outliers final: 0 residues processed: 115 average time/residue: 1.6072 time to fit residues: 189.8931 Evaluate side-chains 112 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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: 10.0000 chunk 29 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.107064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.086435 restraints weight = 5309.113| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.00 r_work: 0.3225 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4640 Z= 0.312 Angle : 0.652 10.992 6308 Z= 0.348 Chirality : 0.051 0.129 800 Planarity : 0.003 0.018 760 Dihedral : 6.634 28.845 932 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.79 % Allowed : 17.26 % Favored : 81.94 % 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: -2.31 (0.32), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 239 PHE 0.013 0.003 PHE D 171 TYR 0.016 0.002 TYR B 143 ARG 0.002 0.000 ARG B 180 ********************** 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: 4 poor density : 112 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 LYS cc_start: 0.8416 (mtpt) cc_final: 0.8095 (mtpt) REVERT: B 192 MET cc_start: 0.8332 (mtp) cc_final: 0.7969 (mtm) REVERT: D 139 LYS cc_start: 0.8229 (ttmt) cc_final: 0.6916 (tppt) REVERT: D 140 ARG cc_start: 0.7399 (tpt170) cc_final: 0.7181 (tpt170) REVERT: D 192 MET cc_start: 0.8685 (mtp) cc_final: 0.8363 (mtm) REVERT: D 209 TYR cc_start: 0.7963 (m-80) cc_final: 0.7616 (m-80) outliers start: 4 outliers final: 1 residues processed: 114 average time/residue: 1.5340 time to fit residues: 179.7687 Evaluate side-chains 112 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 249 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 0.4980 chunk 21 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN A 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.107399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.086622 restraints weight = 5351.983| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.02 r_work: 0.3223 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 4640 Z= 0.295 Angle : 0.652 10.974 6308 Z= 0.347 Chirality : 0.052 0.146 800 Planarity : 0.003 0.019 760 Dihedral : 6.592 28.935 932 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.79 % Allowed : 16.67 % 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: -2.31 (0.32), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 239 PHE 0.013 0.003 PHE D 171 TYR 0.016 0.002 TYR B 143 ARG 0.002 0.000 ARG B 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4482.74 seconds wall clock time: 77 minutes 11.95 seconds (4631.95 seconds total)