Starting phenix.real_space_refine on Sun Mar 10 17:17:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u13_26276/03_2024/7u13_26276.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u13_26276/03_2024/7u13_26276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u13_26276/03_2024/7u13_26276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u13_26276/03_2024/7u13_26276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u13_26276/03_2024/7u13_26276.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u13_26276/03_2024/7u13_26276.pdb" } resolution = 2.9 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= 0.001 sd= 0.003 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 21 5.16 5 C 2202 2.51 5 N 531 2.21 5 O 702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 241": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3456 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} Conformer: "B" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} bond proxies already assigned to first conformer: 1094 Chain: "B" Number of atoms: 1096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} Conformer: "B" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} bond proxies already assigned to first conformer: 1094 Chain: "C" Number of atoms: 1096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} Conformer: "B" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} bond proxies already assigned to first conformer: 1094 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 Chain: "B" 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 Chain: "C" 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 Time building chain proxies: 3.81, per 1000 atoms: 1.10 Number of scatterers: 3456 At special positions: 0 Unit cell: (97.734, 117.066, 31.146, 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 21 16.00 O 702 8.00 N 531 7.00 C 2202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 183 " " NAG A 302 " - " ASN A 151 " " NAG A 303 " - " ASN A 145 " " NAG A 304 " - " ASN A 164 " " NAG B 301 " - " ASN B 183 " " NAG B 302 " - " ASN B 151 " " NAG B 303 " - " ASN B 145 " " NAG B 304 " - " ASN B 164 " " NAG C 301 " - " ASN C 183 " " NAG C 302 " - " ASN C 151 " " NAG C 303 " - " ASN C 145 " " NAG C 304 " - " ASN C 164 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 1.3 seconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 68.9% 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 122 through 125 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 removed outlier: 6.322A pdb=" N LYS A 129 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N TYR B 132 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ALA A 131 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER B 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 131 removed outlier: 6.322A pdb=" N LYS A 129 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N TYR B 132 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ALA A 131 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER B 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER B 130 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA C 131 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR B 132 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 177 removed outlier: 9.050A pdb=" N THR A 141 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N LEU B 144 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N TYR A 143 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N ILE B 146 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN A 145 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ASN B 148 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR A 147 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU B 150 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR A 149 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ILE B 152 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN A 151 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASN B 154 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR A 153 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASN B 156 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN A 155 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N TYR B 158 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR A 157 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL B 160 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER A 159 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL B 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLU A 161 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N ASN B 164 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N GLU A 163 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 10.042A pdb=" N THR B 166 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 165 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N GLN B 168 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 167 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLN B 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 169 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N SER B 172 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE A 171 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N THR B 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS A 173 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE B 176 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 175 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N THR B 141 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N LEU C 144 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TYR B 143 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N ILE C 146 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN B 145 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASN C 148 " --> pdb=" O ASN B 145 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR B 147 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LEU C 150 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR B 149 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE C 152 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN B 151 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ASN C 154 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR B 153 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASN C 156 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN B 155 " --> pdb=" O ASN C 156 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N TYR C 158 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR B 157 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL C 160 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER B 159 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL C 162 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLU B 161 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N ASN C 164 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N GLU B 163 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N THR C 166 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 165 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLN C 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA B 167 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLN C 170 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL B 169 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER C 172 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE B 171 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N THR C 174 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS B 173 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ILE C 176 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 175 " --> pdb=" O ILE C 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.630A pdb=" N ARG A 180 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG B 180 " --> pdb=" O LEU C 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 184 through 187 removed outlier: 6.458A pdb=" N THR A 185 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR B 185 " --> pdb=" O ILE C 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 198 removed outlier: 8.929A pdb=" N MET A 192 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N ILE B 195 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLN A 194 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N TYR B 197 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP A 196 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N MET B 192 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N ILE C 195 " --> pdb=" O MET B 192 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLN B 194 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N TYR C 197 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP B 196 " --> pdb=" O TYR C 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.278A pdb=" N VAL A 202 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL B 202 " --> pdb=" O ILE C 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 209 through 219 removed outlier: 6.960A pdb=" N MET A 210 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR B 211 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASP A 212 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE B 213 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N MET B 210 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR C 211 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP B 212 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE C 213 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 222 through 228 removed outlier: 6.853A pdb=" N ASN B 223 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN C 223 " --> pdb=" O HIS B 222 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 233 through 245 removed outlier: 6.470A pdb=" N THR A 234 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N PHE B 237 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR A 236 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N HIS B 239 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY A 238 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLU B 241 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER A 240 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ILE B 243 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN A 242 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLN B 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER A 244 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 249 through 253 removed outlier: 6.871A pdb=" N TYR B 250 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR C 250 " --> pdb=" O GLN B 249 " (cutoff:3.500A) 53 hydrogen bonds defined for protein. 156 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: 0.85 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 9 1.21 - 1.36: 1059 1.36 - 1.51: 1090 1.51 - 1.66: 1322 1.66 - 1.81: 36 Bond restraints: 3516 Sorted by residual: bond pdb=" CG PRO C 189 " pdb=" CD PRO C 189 " ideal model delta sigma weight residual 1.503 1.173 0.330 3.40e-02 8.65e+02 9.43e+01 bond pdb=" CG PRO B 189 " pdb=" CD PRO B 189 " ideal model delta sigma weight residual 1.503 1.173 0.330 3.40e-02 8.65e+02 9.40e+01 bond pdb=" CG PRO A 189 " pdb=" CD PRO A 189 " ideal model delta sigma weight residual 1.503 1.174 0.329 3.40e-02 8.65e+02 9.35e+01 bond pdb=" CB PRO A 189 " pdb=" CG PRO A 189 " ideal model delta sigma weight residual 1.492 1.063 0.429 5.00e-02 4.00e+02 7.38e+01 bond pdb=" CB PRO B 189 " pdb=" CG PRO B 189 " ideal model delta sigma weight residual 1.492 1.063 0.429 5.00e-02 4.00e+02 7.38e+01 ... (remaining 3511 not shown) Histogram of bond angle deviations from ideal: 73.84 - 95.06: 6 95.06 - 116.29: 2463 116.29 - 137.51: 2316 137.51 - 158.73: 0 158.73 - 179.96: 3 Bond angle restraints: 4788 Sorted by residual: angle pdb=" CB PRO A 189 " pdb=" CG PRO A 189 " pdb=" CD PRO A 189 " ideal model delta sigma weight residual 106.10 179.96 -73.86 3.20e+00 9.77e-02 5.33e+02 angle pdb=" CB PRO B 189 " pdb=" CG PRO B 189 " pdb=" CD PRO B 189 " ideal model delta sigma weight residual 106.10 179.92 -73.82 3.20e+00 9.77e-02 5.32e+02 angle pdb=" CB PRO C 189 " pdb=" CG PRO C 189 " pdb=" CD PRO C 189 " ideal model delta sigma weight residual 106.10 179.89 -73.79 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO A 189 " pdb=" CD PRO A 189 " pdb=" CG PRO A 189 " ideal model delta sigma weight residual 103.20 73.84 29.36 1.50e+00 4.44e-01 3.83e+02 angle pdb=" N PRO C 189 " pdb=" CD PRO C 189 " pdb=" CG PRO C 189 " ideal model delta sigma weight residual 103.20 73.95 29.25 1.50e+00 4.44e-01 3.80e+02 ... (remaining 4783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.07: 2068 26.07 - 52.13: 171 52.13 - 78.20: 18 78.20 - 104.27: 10 104.27 - 130.33: 4 Dihedral angle restraints: 2271 sinusoidal: 1038 harmonic: 1233 Sorted by residual: dihedral pdb=" N PRO A 189 " pdb=" CG PRO A 189 " pdb=" CD PRO A 189 " pdb=" CB PRO A 189 " ideal model delta sinusoidal sigma weight residual -30.00 -160.33 130.33 1 1.50e+01 4.44e-03 7.03e+01 dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 253 " pdb=" CB CYS A 253 " ideal model delta sinusoidal sigma weight residual 93.00 33.46 59.54 1 1.00e+01 1.00e-02 4.73e+01 dihedral pdb=" CB CYS B 214 " pdb=" SG CYS B 214 " pdb=" SG CYS B 253 " pdb=" CB CYS B 253 " ideal model delta sinusoidal sigma weight residual 93.00 33.48 59.52 1 1.00e+01 1.00e-02 4.73e+01 ... (remaining 2268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 438 0.072 - 0.143: 139 0.143 - 0.215: 26 0.215 - 0.286: 0 0.286 - 0.358: 3 Chirality restraints: 606 Sorted by residual: chirality pdb=" CB ILE C 203 " pdb=" CA ILE C 203 " pdb=" CG1 ILE C 203 " pdb=" CG2 ILE C 203 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CB ILE A 203 " pdb=" CA ILE A 203 " pdb=" CG1 ILE A 203 " pdb=" CG2 ILE A 203 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CB ILE B 203 " pdb=" CA ILE B 203 " pdb=" CG1 ILE B 203 " pdb=" CG2 ILE B 203 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 603 not shown) Planarity restraints: 591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 157 " 0.008 2.00e-02 2.50e+03 1.44e-02 4.15e+00 pdb=" CG TYR A 157 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 157 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 157 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 157 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 157 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 157 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 157 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 157 " 0.009 2.00e-02 2.50e+03 1.43e-02 4.11e+00 pdb=" CG TYR B 157 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 157 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 157 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 157 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 157 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 157 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 157 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 157 " 0.009 2.00e-02 2.50e+03 1.43e-02 4.09e+00 pdb=" CG TYR C 157 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR C 157 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR C 157 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 157 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 157 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 157 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 157 " -0.000 2.00e-02 2.50e+03 ... (remaining 588 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 82 2.68 - 3.23: 3267 3.23 - 3.79: 5409 3.79 - 4.34: 6959 4.34 - 4.90: 12721 Nonbonded interactions: 28438 Sorted by model distance: nonbonded pdb=" OH TYR A 197 " pdb=" NZ LYS B 220 " model vdw 2.120 2.520 nonbonded pdb=" NE2 GLN C 229 " pdb=" OG1 THR C 234 " model vdw 2.139 2.520 nonbonded pdb=" NE2 GLN B 229 " pdb=" OG1 THR B 234 " model vdw 2.139 2.520 nonbonded pdb=" NE2 GLN A 229 " pdb=" OG1 THR A 234 " model vdw 2.140 2.520 nonbonded pdb=" OH TYR B 197 " pdb=" NZ LYS C 220 " model vdw 2.168 2.520 ... (remaining 28433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 120 through 210 or resid 212 through 254 or resid 301 thro \ ugh 304)) selection = (chain 'B' and (resid 120 through 210 or resid 212 through 254 or resid 301 thro \ ugh 304)) selection = (chain 'C' and (resid 120 through 210 or resid 212 through 254 or resid 301 thro \ ugh 304)) } 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=0.50 max=1.00 mean=0.99 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.010 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.490 Find NCS groups from input model: 0.220 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:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4696 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 : 0.018 0.429 3516 Z= 1.157 Angle : 2.431 73.856 4788 Z= 1.083 Chirality : 0.071 0.358 606 Planarity : 0.006 0.049 579 Dihedral : 19.232 130.333 1476 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 29.95 Ramachandran Plot: Outliers : 0.75 % Allowed : 11.28 % Favored : 87.97 % Rotamer: Outliers : 6.30 % Allowed : 3.15 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -3.06 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 222 PHE 0.016 0.004 PHE A 171 TYR 0.033 0.005 TYR A 157 ARG 0.004 0.001 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.4399 (mmm) cc_final: 0.3481 (ptt) REVERT: B 231 THR cc_start: 0.6681 (p) cc_final: 0.6419 (p) REVERT: C 219 ILE cc_start: 0.6120 (OUTLIER) cc_final: 0.5797 (mm) outliers start: 24 outliers final: 9 residues processed: 136 average time/residue: 0.8865 time to fit residues: 124.6749 Evaluate side-chains 75 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 219 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN C 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 moved from start: 0.8029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 3516 Z= 0.442 Angle : 1.066 10.219 4788 Z= 0.566 Chirality : 0.066 0.351 606 Planarity : 0.006 0.060 579 Dihedral : 16.576 109.325 729 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 7.87 % Allowed : 19.42 % Favored : 72.70 % 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: -3.87 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS A 239 PHE 0.015 0.003 PHE A 171 TYR 0.025 0.004 TYR C 248 ARG 0.003 0.001 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 87 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.4704 (mmm) cc_final: 0.1821 (ptt) REVERT: A 236 TYR cc_start: 0.5610 (p90) cc_final: 0.3128 (t80) REVERT: A 245 GLN cc_start: 0.7211 (mp10) cc_final: 0.6268 (tt0) REVERT: B 239 HIS cc_start: 0.6871 (OUTLIER) cc_final: 0.6136 (t70) REVERT: C 216 LEU cc_start: 0.8202 (mm) cc_final: 0.7419 (tt) REVERT: C 250 TYR cc_start: 0.5810 (OUTLIER) cc_final: 0.4847 (p90) outliers start: 30 outliers final: 6 residues processed: 105 average time/residue: 0.7530 time to fit residues: 82.4542 Evaluate side-chains 78 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5434 moved from start: 0.8525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3516 Z= 0.304 Angle : 0.950 10.716 4788 Z= 0.494 Chirality : 0.060 0.310 606 Planarity : 0.004 0.037 579 Dihedral : 14.566 107.895 711 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 5.25 % Allowed : 27.82 % Favored : 66.93 % 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: -3.85 (0.33), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS C 239 PHE 0.014 0.002 PHE A 171 TYR 0.015 0.002 TYR C 158 ARG 0.001 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.0679 (tpt) cc_final: -0.0175 (tpt) REVERT: A 210 MET cc_start: 0.4886 (mmm) cc_final: 0.2440 (ptt) REVERT: B 242 GLN cc_start: 0.6901 (OUTLIER) cc_final: 0.6428 (mt0) REVERT: C 250 TYR cc_start: 0.5669 (OUTLIER) cc_final: 0.4979 (p90) outliers start: 20 outliers final: 6 residues processed: 95 average time/residue: 0.7868 time to fit residues: 77.9461 Evaluate side-chains 79 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5667 moved from start: 1.0123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 3516 Z= 0.455 Angle : 1.107 11.062 4788 Z= 0.573 Chirality : 0.067 0.385 606 Planarity : 0.005 0.026 579 Dihedral : 15.087 104.870 711 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % Rotamer: Outliers : 7.61 % Allowed : 28.35 % Favored : 64.04 % 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: -4.41 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 239 PHE 0.014 0.002 PHE A 171 TYR 0.022 0.003 TYR C 125 ARG 0.002 0.001 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 70 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 135 TYR cc_start: 0.5545 (OUTLIER) cc_final: 0.4806 (p90) REVERT: A 184 ILE cc_start: 0.3800 (OUTLIER) cc_final: 0.3435 (pp) REVERT: A 219 ILE cc_start: 0.3638 (OUTLIER) cc_final: 0.2774 (pp) REVERT: A 242 GLN cc_start: 0.6472 (OUTLIER) cc_final: 0.5760 (mt0) REVERT: B 242 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6693 (mt0) REVERT: C 224 ILE cc_start: 0.3569 (OUTLIER) cc_final: 0.2839 (pp) REVERT: C 237 PHE cc_start: 0.4746 (t80) cc_final: 0.4433 (m-80) outliers start: 29 outliers final: 10 residues processed: 89 average time/residue: 0.7444 time to fit residues: 69.0936 Evaluate side-chains 80 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN A 249 GLN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5650 moved from start: 1.0641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 3516 Z= 0.363 Angle : 1.007 9.315 4788 Z= 0.519 Chirality : 0.064 0.324 606 Planarity : 0.004 0.023 579 Dihedral : 14.739 105.149 711 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % Rotamer: Outliers : 7.09 % Allowed : 30.18 % Favored : 62.73 % 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: -4.55 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 239 PHE 0.021 0.002 PHE A 237 TYR 0.020 0.002 TYR C 125 ARG 0.002 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 72 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 135 TYR cc_start: 0.5654 (OUTLIER) cc_final: 0.4967 (p90) REVERT: A 184 ILE cc_start: 0.3720 (OUTLIER) cc_final: 0.3404 (pp) REVERT: A 207 MET cc_start: 0.1060 (tpt) cc_final: 0.0755 (tmt) REVERT: A 219 ILE cc_start: 0.3581 (OUTLIER) cc_final: 0.2710 (pp) REVERT: B 242 GLN cc_start: 0.6897 (OUTLIER) cc_final: 0.6476 (mt0) REVERT: B 249 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6505 (tt0) REVERT: C 237 PHE cc_start: 0.4659 (t80) cc_final: 0.4409 (m-80) outliers start: 27 outliers final: 10 residues processed: 87 average time/residue: 0.7727 time to fit residues: 70.1415 Evaluate side-chains 85 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.0050 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5464 moved from start: 1.0555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3516 Z= 0.238 Angle : 0.914 12.046 4788 Z= 0.462 Chirality : 0.058 0.219 606 Planarity : 0.003 0.020 579 Dihedral : 13.408 103.022 711 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 5.25 % Allowed : 32.55 % Favored : 62.20 % 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: -4.37 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS C 239 PHE 0.019 0.002 PHE A 237 TYR 0.013 0.001 TYR B 135 ARG 0.001 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 184 ILE cc_start: 0.3637 (OUTLIER) cc_final: 0.3386 (pp) REVERT: A 219 ILE cc_start: 0.3014 (OUTLIER) cc_final: 0.2136 (pp) REVERT: A 245 GLN cc_start: 0.6862 (mp10) cc_final: 0.6043 (tt0) REVERT: B 242 GLN cc_start: 0.6667 (OUTLIER) cc_final: 0.6240 (mt0) REVERT: C 242 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6581 (mt0) REVERT: C 250 TYR cc_start: 0.5679 (OUTLIER) cc_final: 0.5165 (p90) outliers start: 20 outliers final: 8 residues processed: 90 average time/residue: 0.8165 time to fit residues: 76.4981 Evaluate side-chains 87 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN C 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 1.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3516 Z= 0.320 Angle : 0.970 9.166 4788 Z= 0.499 Chirality : 0.061 0.263 606 Planarity : 0.004 0.024 579 Dihedral : 13.250 97.948 711 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 7.09 % Allowed : 31.50 % Favored : 61.42 % 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: -4.37 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS C 239 PHE 0.025 0.003 PHE C 237 TYR 0.019 0.002 TYR C 125 ARG 0.002 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 70 time to evaluate : 0.369 Fit side-chains REVERT: A 184 ILE cc_start: 0.3689 (OUTLIER) cc_final: 0.3390 (pp) REVERT: A 207 MET cc_start: 0.1435 (tpt) cc_final: 0.1014 (tmt) REVERT: A 219 ILE cc_start: 0.2897 (OUTLIER) cc_final: 0.2044 (pp) REVERT: A 236 TYR cc_start: 0.6404 (OUTLIER) cc_final: 0.3353 (t80) REVERT: B 242 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6536 (mt0) REVERT: C 216 LEU cc_start: 0.7387 (mm) cc_final: 0.7166 (tp) REVERT: C 242 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6744 (mt0) outliers start: 27 outliers final: 10 residues processed: 87 average time/residue: 0.8772 time to fit residues: 79.2544 Evaluate side-chains 82 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN C 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5500 moved from start: 1.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3516 Z= 0.247 Angle : 0.947 12.939 4788 Z= 0.477 Chirality : 0.059 0.222 606 Planarity : 0.003 0.027 579 Dihedral : 12.522 94.871 711 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 4.72 % Allowed : 33.33 % Favored : 61.94 % 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: -4.21 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS C 239 PHE 0.021 0.002 PHE A 237 TYR 0.013 0.002 TYR B 135 ARG 0.001 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 0.385 Fit side-chains REVERT: A 184 ILE cc_start: 0.3592 (OUTLIER) cc_final: 0.3352 (pp) REVERT: A 219 ILE cc_start: 0.3048 (OUTLIER) cc_final: 0.2173 (pp) REVERT: A 236 TYR cc_start: 0.6223 (OUTLIER) cc_final: 0.3276 (t80) REVERT: A 245 GLN cc_start: 0.6945 (mp10) cc_final: 0.5999 (tt0) REVERT: B 242 GLN cc_start: 0.6751 (OUTLIER) cc_final: 0.6459 (mt0) REVERT: C 242 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6813 (mt0) REVERT: C 250 TYR cc_start: 0.5658 (OUTLIER) cc_final: 0.5054 (p90) outliers start: 18 outliers final: 11 residues processed: 80 average time/residue: 0.9531 time to fit residues: 78.9769 Evaluate side-chains 84 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.0060 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 0.0770 chunk 3 optimal weight: 7.9990 overall best weight: 1.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5466 moved from start: 1.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3516 Z= 0.237 Angle : 0.920 12.855 4788 Z= 0.462 Chirality : 0.058 0.210 606 Planarity : 0.004 0.029 579 Dihedral : 11.896 91.947 711 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 4.20 % Allowed : 35.17 % Favored : 60.63 % 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: -4.13 (0.33), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 239 PHE 0.024 0.003 PHE C 237 TYR 0.009 0.001 TYR B 125 ARG 0.001 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.442 Fit side-chains REVERT: A 184 ILE cc_start: 0.3661 (OUTLIER) cc_final: 0.3447 (pp) REVERT: A 219 ILE cc_start: 0.3028 (OUTLIER) cc_final: 0.2422 (pp) REVERT: A 236 TYR cc_start: 0.6308 (OUTLIER) cc_final: 0.3292 (t80) REVERT: A 245 GLN cc_start: 0.6802 (mp10) cc_final: 0.6001 (tt0) REVERT: B 242 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.6395 (mt0) REVERT: C 227 MET cc_start: 0.6056 (mmt) cc_final: 0.5701 (mmt) REVERT: C 250 TYR cc_start: 0.5492 (OUTLIER) cc_final: 0.4842 (p90) outliers start: 16 outliers final: 7 residues processed: 82 average time/residue: 0.8723 time to fit residues: 74.2373 Evaluate side-chains 80 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.0020 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 overall best weight: 1.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN C 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5462 moved from start: 1.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3516 Z= 0.249 Angle : 0.947 13.290 4788 Z= 0.475 Chirality : 0.058 0.210 606 Planarity : 0.003 0.030 579 Dihedral : 11.537 88.609 711 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 3.67 % Allowed : 35.70 % Favored : 60.63 % 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: -4.16 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 239 PHE 0.019 0.002 PHE A 237 TYR 0.014 0.002 TYR B 135 ARG 0.001 0.000 ARG C 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.344 Fit side-chains REVERT: A 184 ILE cc_start: 0.3747 (OUTLIER) cc_final: 0.3501 (pp) REVERT: A 236 TYR cc_start: 0.6320 (OUTLIER) cc_final: 0.3270 (t80) REVERT: B 242 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6578 (mt0) REVERT: C 237 PHE cc_start: 0.6330 (m-10) cc_final: 0.4590 (t80) REVERT: C 250 TYR cc_start: 0.5469 (OUTLIER) cc_final: 0.4817 (p90) outliers start: 14 outliers final: 7 residues processed: 78 average time/residue: 0.8490 time to fit residues: 68.7736 Evaluate side-chains 78 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5653 r_free = 0.5653 target = 0.315809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.6006 r_free = 0.6006 target = 0.280341 restraints weight = 21421.896| |-----------------------------------------------------------------------------| r_work (start): 0.5556 rms_B_bonded: 4.16 r_work: 0.5928 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.5866 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.5866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5491 r_free = 0.5491 target_work(ls_wunit_k1) = 0.295 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5488 r_free = 0.5488 target_work(ls_wunit_k1) = 0.295 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.5488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5582 moved from start: 1.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3516 Z= 0.266 Angle : 0.959 12.895 4788 Z= 0.479 Chirality : 0.058 0.218 606 Planarity : 0.004 0.030 579 Dihedral : 11.301 84.042 711 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 3.67 % Allowed : 37.27 % Favored : 59.06 % 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: -4.19 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 239 PHE 0.019 0.003 PHE A 237 TYR 0.014 0.002 TYR C 125 ARG 0.001 0.000 ARG A 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1906.96 seconds wall clock time: 34 minutes 31.71 seconds (2071.71 seconds total)