Starting phenix.real_space_refine on Fri Dec 8 01:51:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvf_14176/12_2023/7qvf_14176.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvf_14176/12_2023/7qvf_14176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvf_14176/12_2023/7qvf_14176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvf_14176/12_2023/7qvf_14176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvf_14176/12_2023/7qvf_14176.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qvf_14176/12_2023/7qvf_14176.pdb" } resolution = 3.64 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 42 5.16 5 C 4164 2.51 5 N 1038 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 206": "OE1" <-> "OE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 206": "OE1" <-> "OE2" Residue "F GLU 246": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6516 Number of models: 1 Model: "" Number of chains: 6 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: "B" 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: "C" 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: "D" 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: "E" 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: "F" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Time building chain proxies: 3.99, per 1000 atoms: 0.61 Number of scatterers: 6516 At special positions: 0 Unit cell: (175.95, 204.7, 36.8, 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 42 16.00 O 1272 8.00 N 1038 7.00 C 4164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.05 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.05 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 253 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 253 " distance=2.05 Simple disulfide: pdb=" SG CYS F 214 " - pdb=" SG CYS F 253 " distance=2.05 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 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.5 seconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 34 sheets defined 0.0% alpha, 60.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 126 removed outlier: 6.737A pdb=" N ASP A 122 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP B 122 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.823A pdb=" N VAL A 133 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 133 " --> pdb=" O SER C 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 137 through 139 removed outlier: 6.647A pdb=" N GLN A 138 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N VAL B 137 " --> pdb=" O GLN C 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 142 through 144 Processing sheet with id=AA6, first strand: chain 'A' and resid 147 through 153 Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 160 Processing sheet with id=AA8, first strand: chain 'A' and resid 163 through 176 removed outlier: 6.867A pdb=" N ASN A 164 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE B 165 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 166 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN B 164 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE C 165 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR B 166 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AB1, first strand: chain 'A' and resid 184 through 187 removed outlier: 6.447A pdb=" N ILE A 184 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE B 187 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 186 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 184 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE C 187 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 186 " --> pdb=" O ILE C 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 192 through 193 removed outlier: 6.589A pdb=" N MET A 192 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET B 192 " --> pdb=" O LYS C 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 196 through 198 removed outlier: 6.419A pdb=" N TYR A 197 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR B 197 " --> pdb=" O THR C 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 201 through 206 Processing sheet with id=AB5, first strand: chain 'A' and resid 209 through 213 Processing sheet with id=AB6, first strand: chain 'A' and resid 216 through 219 Processing sheet with id=AB7, first strand: chain 'A' and resid 222 through 228 removed outlier: 5.995A pdb=" N ASN A 223 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 226 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 225 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N MET B 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET A 227 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN B 223 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU C 226 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N MET C 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET B 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 231 through 253 removed outlier: 5.752A pdb=" N THR A 231 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR B 234 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR A 233 " --> pdb=" O THR B 234 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N TYR B 236 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR A 235 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLY B 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N PHE A 237 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N SER B 240 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS A 239 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N GLN B 242 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU A 241 " --> pdb=" O GLN B 242 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N SER B 244 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 243 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLU B 246 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN A 245 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N TYR B 248 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG A 247 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TYR B 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N GLN A 249 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP B 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N VAL A 251 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N THR B 231 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR C 234 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR B 233 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N TYR C 236 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR B 235 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLY C 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE B 237 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N SER C 240 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS B 239 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N GLN C 242 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU B 241 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N SER C 244 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE B 243 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLU C 246 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN B 245 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N TYR C 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG B 247 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR C 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N GLN B 249 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP C 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N VAL B 251 " --> pdb=" O ASP C 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 121 through 126 removed outlier: 6.737A pdb=" N ASP D 122 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE D 121 " --> pdb=" O ASP F 122 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N LYS F 124 " --> pdb=" O ILE D 121 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL D 123 " --> pdb=" O LYS F 124 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE F 126 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR D 125 " --> pdb=" O ILE F 126 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 129 through 130 removed outlier: 6.510A pdb=" N LYS D 129 " --> pdb=" O SER F 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 133 through 134 removed outlier: 6.893A pdb=" N VAL D 133 " --> pdb=" O SER E 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 137 through 139 removed outlier: 8.555A pdb=" N VAL D 137 " --> pdb=" O GLN E 138 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLN F 138 " --> pdb=" O VAL D 137 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 142 through 144 removed outlier: 6.148A pdb=" N ILE D 142 " --> pdb=" O TYR F 143 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 147 through 153 removed outlier: 6.182A pdb=" N THR D 147 " --> pdb=" O ASN F 148 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU F 150 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR D 149 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE F 152 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN D 151 " --> pdb=" O ILE F 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 156 through 160 removed outlier: 6.511A pdb=" N TYR D 157 " --> pdb=" O TYR F 158 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL F 160 " --> pdb=" O TYR D 157 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER D 159 " --> pdb=" O VAL F 160 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 163 through 176 removed outlier: 6.897A pdb=" N ASN D 164 " --> pdb=" O GLU E 163 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE E 165 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR D 166 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N GLU D 163 " --> pdb=" O ASN F 164 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N THR F 166 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE D 165 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N GLN F 168 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA D 167 " --> pdb=" O GLN F 168 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N GLN F 170 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL D 169 " --> pdb=" O GLN F 170 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER F 172 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE D 171 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR F 174 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS D 173 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ILE F 176 " --> pdb=" O LYS D 173 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 175 " --> pdb=" O ILE F 176 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 180 through 181 removed outlier: 6.520A pdb=" N ARG D 180 " --> pdb=" O LEU F 181 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.521A pdb=" N ILE D 184 " --> pdb=" O THR E 185 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE E 187 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE D 186 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 192 through 193 removed outlier: 6.577A pdb=" N MET D 192 " --> pdb=" O LYS E 193 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 196 through 198 removed outlier: 6.400A pdb=" N TYR D 197 " --> pdb=" O THR E 198 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 201 through 206 removed outlier: 6.314A pdb=" N VAL D 202 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLU F 205 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA D 204 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 209 through 213 removed outlier: 6.394A pdb=" N TYR D 209 " --> pdb=" O MET F 210 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASP F 212 " --> pdb=" O TYR D 209 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR D 211 " --> pdb=" O ASP F 212 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 216 through 219 removed outlier: 6.275A pdb=" N LEU D 216 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE F 219 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER D 218 " --> pdb=" O ILE F 219 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 222 through 228 removed outlier: 6.230A pdb=" N ASN D 223 " --> pdb=" O ILE E 224 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU E 226 " --> pdb=" O ASN D 223 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL D 225 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N MET E 228 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET D 227 " --> pdb=" O MET E 228 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN F 223 " --> pdb=" O HIS D 222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 231 through 253 removed outlier: 5.687A pdb=" N THR D 231 " --> pdb=" O VAL E 232 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR E 234 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR D 233 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N TYR E 236 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR D 235 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLY E 238 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE D 237 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N SER E 240 " --> pdb=" O PHE D 237 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS D 239 " --> pdb=" O SER E 240 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N GLN E 242 " --> pdb=" O HIS D 239 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU D 241 " --> pdb=" O GLN E 242 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N SER E 244 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE D 243 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N GLU E 246 " --> pdb=" O ILE D 243 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN D 245 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N TYR E 248 " --> pdb=" O GLN D 245 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG D 247 " --> pdb=" O TYR E 248 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR E 250 " --> pdb=" O ARG D 247 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLN D 249 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ASP E 252 " --> pdb=" O GLN D 249 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N VAL D 251 " --> pdb=" O ASP E 252 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL D 232 " --> pdb=" O THR F 231 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL F 251 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASP D 252 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N CYS F 253 " --> pdb=" O ASP D 252 " (cutoff:3.500A) 151 hydrogen bonds defined for protein. 453 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: 1.93 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1812 1.33 - 1.45: 1086 1.45 - 1.57: 3654 1.57 - 1.69: 0 1.69 - 1.82: 72 Bond restraints: 6624 Sorted by residual: bond pdb=" CZ ARG C 247 " pdb=" NH2 ARG C 247 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.42e+00 bond pdb=" CZ ARG E 247 " pdb=" NH2 ARG E 247 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.22e+00 bond pdb=" CZ ARG D 247 " pdb=" NH2 ARG D 247 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.69e+00 bond pdb=" CZ ARG B 247 " pdb=" NH2 ARG B 247 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.56e+00 bond pdb=" CZ ARG D 180 " pdb=" NH2 ARG D 180 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.86e+00 ... (remaining 6619 not shown) Histogram of bond angle deviations from ideal: 98.06 - 104.31: 90 104.31 - 110.55: 1552 110.55 - 116.79: 2715 116.79 - 123.03: 3867 123.03 - 129.27: 782 Bond angle restraints: 9006 Sorted by residual: angle pdb=" N GLU C 246 " pdb=" CA GLU C 246 " pdb=" C GLU C 246 " ideal model delta sigma weight residual 108.55 120.11 -11.56 1.62e+00 3.81e-01 5.09e+01 angle pdb=" N GLU E 246 " pdb=" CA GLU E 246 " pdb=" C GLU E 246 " ideal model delta sigma weight residual 108.55 120.09 -11.54 1.62e+00 3.81e-01 5.08e+01 angle pdb=" CB ASN A 183 " pdb=" CG ASN A 183 " pdb=" ND2 ASN A 183 " ideal model delta sigma weight residual 116.40 106.14 10.26 1.50e+00 4.44e-01 4.68e+01 angle pdb=" CB ASN F 183 " pdb=" CG ASN F 183 " pdb=" ND2 ASN F 183 " ideal model delta sigma weight residual 116.40 106.15 10.25 1.50e+00 4.44e-01 4.67e+01 angle pdb=" CA ASP B 136 " pdb=" CB ASP B 136 " pdb=" CG ASP B 136 " ideal model delta sigma weight residual 112.60 119.34 -6.74 1.00e+00 1.00e+00 4.54e+01 ... (remaining 9001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 3626 17.73 - 35.45: 268 35.45 - 53.18: 54 53.18 - 70.91: 14 70.91 - 88.63: 28 Dihedral angle restraints: 3990 sinusoidal: 1554 harmonic: 2436 Sorted by residual: dihedral pdb=" CA ILE C 152 " pdb=" C ILE C 152 " pdb=" N THR C 153 " pdb=" CA THR C 153 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ILE B 152 " pdb=" C ILE B 152 " pdb=" N THR B 153 " pdb=" CA THR B 153 " ideal model delta harmonic sigma weight residual 180.00 151.42 28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ILE E 152 " pdb=" C ILE E 152 " pdb=" N THR E 153 " pdb=" CA THR E 153 " ideal model delta harmonic sigma weight residual 180.00 151.42 28.58 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 3987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 695 0.108 - 0.216: 314 0.216 - 0.324: 55 0.324 - 0.432: 12 0.432 - 0.540: 10 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CA GLN E 138 " pdb=" N GLN E 138 " pdb=" C GLN E 138 " pdb=" CB GLN E 138 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.29e+00 chirality pdb=" CA GLN C 138 " pdb=" N GLN C 138 " pdb=" C GLN C 138 " pdb=" CB GLN C 138 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" CA GLN D 194 " pdb=" N GLN D 194 " pdb=" C GLN D 194 " pdb=" CB GLN D 194 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.05e+00 ... (remaining 1083 not shown) Planarity restraints: 1116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 143 " -0.138 2.00e-02 2.50e+03 7.16e-02 1.03e+02 pdb=" CG TYR A 143 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR A 143 " 0.065 2.00e-02 2.50e+03 pdb=" CD2 TYR A 143 " 0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR A 143 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR A 143 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 143 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 143 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 143 " 0.138 2.00e-02 2.50e+03 7.15e-02 1.02e+02 pdb=" CG TYR F 143 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR F 143 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 TYR F 143 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR F 143 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR F 143 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR F 143 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR F 143 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 250 " 0.096 2.00e-02 2.50e+03 5.64e-02 6.36e+01 pdb=" CG TYR F 250 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR F 250 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR F 250 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR F 250 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR F 250 " -0.034 2.00e-02 2.50e+03 pdb=" CZ TYR F 250 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 250 " 0.092 2.00e-02 2.50e+03 ... (remaining 1113 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 3273 3.00 - 3.47: 5692 3.47 - 3.95: 10879 3.95 - 4.42: 11354 4.42 - 4.90: 21068 Nonbonded interactions: 52266 Sorted by model distance: nonbonded pdb=" OG SER D 134 " pdb=" OD1 ASP D 136 " model vdw 2.525 2.440 nonbonded pdb=" OG SER B 134 " pdb=" OD1 ASP B 136 " model vdw 2.525 2.440 nonbonded pdb=" OE2 GLU D 241 " pdb=" OG SER E 120 " model vdw 2.528 2.440 nonbonded pdb=" OE2 GLU B 241 " pdb=" OG SER C 120 " model vdw 2.529 2.440 nonbonded pdb=" OG SER D 120 " pdb=" OE2 GLU F 241 " model vdw 2.542 2.440 ... (remaining 52261 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue 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: 14.060 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: 28.120 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.140 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 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 : 0.012 0.047 6624 Z= 0.795 Angle : 2.103 11.556 9006 Z= 1.357 Chirality : 0.125 0.540 1086 Planarity : 0.013 0.095 1116 Dihedral : 15.513 88.633 2412 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.53 % Allowed : 4.76 % Favored : 94.71 % Cbeta Deviations : 2.82 % 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: -2.41 (0.24), residues: 798 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.18), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.005 HIS B 239 PHE 0.032 0.010 PHE F 171 TYR 0.138 0.025 TYR A 143 ARG 0.002 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 335 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 335 average time/residue: 0.2000 time to fit residues: 85.1156 Evaluate side-chains 228 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0688 time to fit residues: 1.2300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.0770 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 249 GLN ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 245 GLN ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6624 Z= 0.258 Angle : 0.769 6.066 9006 Z= 0.422 Chirality : 0.060 0.202 1086 Planarity : 0.003 0.019 1116 Dihedral : 7.118 25.611 894 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.65 % Allowed : 15.48 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.23 (0.25), residues: 798 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 239 PHE 0.010 0.001 PHE B 237 TYR 0.022 0.002 TYR E 143 ARG 0.002 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 233 time to evaluate : 0.863 Fit side-chains outliers start: 20 outliers final: 7 residues processed: 243 average time/residue: 0.2448 time to fit residues: 76.2876 Evaluate side-chains 216 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 209 time to evaluate : 1.707 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0693 time to fit residues: 2.1998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 58 optimal weight: 0.2980 chunk 48 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6624 Z= 0.293 Angle : 0.739 7.905 9006 Z= 0.398 Chirality : 0.056 0.181 1086 Planarity : 0.003 0.028 1116 Dihedral : 6.816 27.729 894 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.12 % Allowed : 18.92 % Favored : 78.97 % 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: -2.27 (0.25), residues: 798 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 239 PHE 0.014 0.002 PHE B 237 TYR 0.018 0.002 TYR C 143 ARG 0.003 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 220 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 222 average time/residue: 0.2170 time to fit residues: 60.7932 Evaluate side-chains 205 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 200 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0655 time to fit residues: 1.6782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 37 optimal weight: 0.1980 chunk 67 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6624 Z= 0.242 Angle : 0.673 7.879 9006 Z= 0.364 Chirality : 0.055 0.185 1086 Planarity : 0.003 0.034 1116 Dihedral : 6.485 27.546 894 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.25 % Allowed : 19.97 % Favored : 77.78 % 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: -2.24 (0.26), residues: 798 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS C 239 PHE 0.010 0.001 PHE D 237 TYR 0.017 0.002 TYR C 143 ARG 0.001 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 221 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 229 average time/residue: 0.2123 time to fit residues: 61.1238 Evaluate side-chains 206 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 199 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1231 time to fit residues: 2.2792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 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 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.6307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6624 Z= 0.363 Angle : 0.762 8.796 9006 Z= 0.405 Chirality : 0.057 0.173 1086 Planarity : 0.003 0.029 1116 Dihedral : 6.572 27.857 894 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.12 % Allowed : 21.43 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.25), residues: 798 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.003 HIS B 239 PHE 0.014 0.002 PHE E 171 TYR 0.019 0.002 TYR D 143 ARG 0.003 0.000 ARG F 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 210 time to evaluate : 0.832 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 215 average time/residue: 0.2209 time to fit residues: 59.5936 Evaluate side-chains 206 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 0.819 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0681 time to fit residues: 2.3638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 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 145 ASN B 145 ASN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.6598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 6624 Z= 0.382 Angle : 0.796 11.487 9006 Z= 0.414 Chirality : 0.057 0.169 1086 Planarity : 0.004 0.040 1116 Dihedral : 6.624 29.383 894 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.38 % Allowed : 22.49 % Favored : 75.13 % 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: -2.45 (0.25), residues: 798 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS B 239 PHE 0.012 0.002 PHE E 171 TYR 0.023 0.002 TYR F 143 ARG 0.003 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 199 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 207 average time/residue: 0.2884 time to fit residues: 73.8192 Evaluate side-chains 197 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0688 time to fit residues: 2.1360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.6763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6624 Z= 0.242 Angle : 0.738 11.272 9006 Z= 0.382 Chirality : 0.055 0.161 1086 Planarity : 0.003 0.035 1116 Dihedral : 6.455 28.214 894 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.32 % Allowed : 23.81 % Favored : 74.87 % 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: -2.43 (0.26), residues: 798 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS B 239 PHE 0.011 0.001 PHE E 171 TYR 0.017 0.002 TYR A 143 ARG 0.001 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 207 time to evaluate : 1.060 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 209 average time/residue: 0.2491 time to fit residues: 65.0575 Evaluate side-chains 195 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0951 time to fit residues: 1.8788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 0.0670 chunk 7 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6624 Z= 0.306 Angle : 0.763 12.369 9006 Z= 0.398 Chirality : 0.055 0.155 1086 Planarity : 0.003 0.035 1116 Dihedral : 6.451 28.284 894 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.06 % Allowed : 25.00 % Favored : 73.94 % 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: -2.47 (0.26), residues: 798 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS B 239 PHE 0.011 0.002 PHE E 171 TYR 0.021 0.002 TYR A 143 ARG 0.002 0.000 ARG F 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 201 time to evaluate : 0.819 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 202 average time/residue: 0.2331 time to fit residues: 58.6446 Evaluate side-chains 198 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0749 time to fit residues: 1.6179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.7055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6624 Z= 0.331 Angle : 0.781 11.478 9006 Z= 0.406 Chirality : 0.056 0.184 1086 Planarity : 0.003 0.034 1116 Dihedral : 6.474 28.712 894 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.93 % Allowed : 25.00 % Favored : 74.07 % 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: -2.50 (0.26), residues: 798 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS B 239 PHE 0.010 0.002 PHE E 171 TYR 0.021 0.002 TYR A 143 ARG 0.003 0.000 ARG F 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 199 time to evaluate : 0.930 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 200 average time/residue: 0.2287 time to fit residues: 57.2900 Evaluate side-chains 192 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0794 time to fit residues: 1.1944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.7209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6624 Z= 0.223 Angle : 0.761 15.339 9006 Z= 0.390 Chirality : 0.055 0.236 1086 Planarity : 0.003 0.031 1116 Dihedral : 6.370 27.205 894 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.66 % Allowed : 27.12 % Favored : 72.22 % 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: -2.43 (0.26), residues: 798 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS B 239 PHE 0.010 0.001 PHE E 171 TYR 0.017 0.001 TYR A 143 ARG 0.002 0.000 ARG B 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 200 time to evaluate : 0.905 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 202 average time/residue: 0.2351 time to fit residues: 59.4044 Evaluate side-chains 191 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0500 time to fit residues: 1.1527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4421 r_free = 0.4421 target = 0.126242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.117565 restraints weight = 15901.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.119520 restraints weight = 6861.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.120710 restraints weight = 3801.117| |-----------------------------------------------------------------------------| r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.7234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6624 Z= 0.332 Angle : 0.805 16.917 9006 Z= 0.414 Chirality : 0.056 0.183 1086 Planarity : 0.003 0.031 1116 Dihedral : 6.436 31.635 894 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.06 % Allowed : 27.25 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.44 (0.26), residues: 798 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS B 239 PHE 0.011 0.002 PHE E 171 TYR 0.019 0.002 TYR F 143 ARG 0.003 0.000 ARG F 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2120.06 seconds wall clock time: 39 minutes 59.82 seconds (2399.82 seconds total)