Starting phenix.real_space_refine on Sun Mar 10 17:17:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u14_26277/03_2024/7u14_26277.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u14_26277/03_2024/7u14_26277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u14_26277/03_2024/7u14_26277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u14_26277/03_2024/7u14_26277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u14_26277/03_2024/7u14_26277.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u14_26277/03_2024/7u14_26277.pdb" } resolution = 4.5 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= 0.003 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 246": "OE1" <-> "OE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "C GLU 246": "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: 3.87, per 1000 atoms: 1.12 Number of scatterers: 3456 At special positions: 0 Unit cell: (98.808, 118.14, 33.294, 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=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.04 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: 1.14 Conformation dependent library (CDL) restraints added in 1.1 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, 60.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 137 removed outlier: 6.384A pdb=" N LYS A 129 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N TYR B 132 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N ALA A 131 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER B 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N VAL A 133 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N ASP B 136 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TYR A 135 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N TYR C 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N ALA B 131 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N SER C 134 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N VAL B 133 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N ASP C 136 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N TYR B 135 " --> pdb=" O ASP C 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 165 removed outlier: 6.948A pdb=" N ILE A 146 " --> pdb=" O ASN B 145 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR B 147 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASN A 148 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR B 149 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU A 150 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASN B 151 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE A 152 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR B 153 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASN A 154 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN B 155 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN A 156 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR B 157 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR A 158 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N SER B 159 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL A 160 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU B 161 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE B 146 " --> pdb=" O ASN C 145 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR C 147 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN B 148 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR C 149 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU B 150 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN C 151 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 152 " --> pdb=" O ASN C 151 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR C 153 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN B 154 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN C 155 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASN B 156 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR C 157 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N TYR B 158 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER C 159 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 160 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU C 161 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.575A pdb=" N ARG A 180 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.570A 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: 6.408A pdb=" N THR A 185 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.430A 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: 6.775A pdb=" N ILE A 195 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP B 196 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR A 197 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR B 198 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE B 195 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP C 196 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR B 197 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR C 198 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.336A pdb=" N VAL A 202 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.379A 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: 6.973A pdb=" N MET A 210 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR B 211 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP A 212 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE B 213 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N MET B 210 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR C 211 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASP B 212 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE C 213 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 225 through 228 Processing sheet with id=AB2, first strand: chain 'A' and resid 233 through 245 removed outlier: 6.605A pdb=" N THR A 234 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N PHE B 237 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR A 236 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N HIS B 239 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY A 238 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLU B 241 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER A 240 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE B 243 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN A 242 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLN B 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER A 244 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR B 234 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N PHE C 237 " --> pdb=" O THR B 234 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR B 236 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N HIS C 239 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY B 238 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N GLU C 241 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER B 240 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE C 243 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN B 242 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLN C 245 " --> pdb=" O GLN B 242 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER B 244 " --> pdb=" O GLN C 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 251 through 253 66 hydrogen bonds defined for protein. 198 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: 0.87 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1011 1.34 - 1.46: 629 1.46 - 1.58: 1840 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 3516 Sorted by residual: bond pdb=" C1 NAG A 304 " pdb=" O5 NAG A 304 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C1 NAG C 304 " pdb=" O5 NAG C 304 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C1 NAG B 304 " pdb=" O5 NAG B 304 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CD GLU A 206 " pdb=" OE1 GLU A 206 " ideal model delta sigma weight residual 1.249 1.214 0.035 1.90e-02 2.77e+03 3.39e+00 bond pdb=" CB VAL C 225 " pdb=" CG2 VAL C 225 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.33e+00 ... (remaining 3511 not shown) Histogram of bond angle deviations from ideal: 99.66 - 105.99: 60 105.99 - 112.32: 1842 112.32 - 118.65: 975 118.65 - 124.98: 1899 124.98 - 131.31: 12 Bond angle restraints: 4788 Sorted by residual: angle pdb=" CA MET C 228 " pdb=" CB MET C 228 " pdb=" CG MET C 228 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 angle pdb=" CA MET A 228 " pdb=" CB MET A 228 " pdb=" CG MET A 228 " ideal model delta sigma weight residual 114.10 121.51 -7.41 2.00e+00 2.50e-01 1.37e+01 angle pdb=" CA MET B 228 " pdb=" CB MET B 228 " pdb=" CG MET B 228 " ideal model delta sigma weight residual 114.10 121.42 -7.32 2.00e+00 2.50e-01 1.34e+01 angle pdb=" CA GLU C 205 " pdb=" CB GLU C 205 " pdb=" CG GLU C 205 " ideal model delta sigma weight residual 114.10 121.18 -7.08 2.00e+00 2.50e-01 1.25e+01 angle pdb=" CA GLU B 205 " pdb=" CB GLU B 205 " pdb=" CG GLU B 205 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 ... (remaining 4783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.61: 2043 24.61 - 49.21: 178 49.21 - 73.82: 29 73.82 - 98.43: 18 98.43 - 123.04: 3 Dihedral angle restraints: 2271 sinusoidal: 1038 harmonic: 1233 Sorted by residual: dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 253 " pdb=" CB CYS C 253 " ideal model delta sinusoidal sigma weight residual 93.00 40.17 52.83 1 1.00e+01 1.00e-02 3.80e+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 40.18 52.82 1 1.00e+01 1.00e-02 3.80e+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 40.24 52.76 1 1.00e+01 1.00e-02 3.79e+01 ... (remaining 2268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 477 0.078 - 0.156: 117 0.156 - 0.234: 9 0.234 - 0.312: 0 0.312 - 0.390: 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 2.26 0.39 2.00e-01 2.50e+01 3.80e+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 2.26 0.38 2.00e-01 2.50e+01 3.69e+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 2.26 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 603 not shown) Planarity restraints: 591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 125 " -0.027 2.00e-02 2.50e+03 2.67e-02 1.43e+01 pdb=" CG TYR C 125 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR C 125 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 125 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR C 125 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR C 125 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 125 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 125 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 125 " -0.027 2.00e-02 2.50e+03 2.66e-02 1.42e+01 pdb=" CG TYR A 125 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR A 125 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 125 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR A 125 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 125 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 125 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 125 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 125 " -0.026 2.00e-02 2.50e+03 2.65e-02 1.41e+01 pdb=" CG TYR B 125 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR B 125 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 125 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 125 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR B 125 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 125 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 125 " 0.000 2.00e-02 2.50e+03 ... (remaining 588 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 1220 2.87 - 3.38: 2979 3.38 - 3.89: 6107 3.89 - 4.39: 6044 4.39 - 4.90: 11905 Nonbonded interactions: 28255 Sorted by model distance: nonbonded pdb=" NZ LYS C 129 " pdb=" OD2 ASP C 136 " model vdw 2.369 2.520 nonbonded pdb=" NZ LYS B 129 " pdb=" OD2 ASP B 136 " model vdw 2.369 2.520 nonbonded pdb=" NZ LYS A 129 " pdb=" OD2 ASP A 136 " model vdw 2.370 2.520 nonbonded pdb=" OH TYR B 236 " pdb=" O HIS B 239 " model vdw 2.423 2.440 nonbonded pdb=" OH TYR A 236 " pdb=" O HIS A 239 " model vdw 2.424 2.440 ... (remaining 28250 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 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: 0.910 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: 4.060 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 15.740 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5068 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 : 0.006 0.074 3516 Z= 0.426 Angle : 0.945 8.455 4788 Z= 0.493 Chirality : 0.066 0.390 606 Planarity : 0.005 0.028 579 Dihedral : 19.585 123.035 1476 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 6.30 % Allowed : 2.36 % Favored : 91.34 % 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: -3.07 (0.38), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 222 PHE 0.020 0.004 PHE B 171 TYR 0.064 0.004 TYR C 125 ARG 0.002 0.000 ARG A 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 81 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 57 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 186 ILE cc_start: 0.7852 (mt) cc_final: 0.7365 (mp) REVERT: A 222 HIS cc_start: 0.5934 (m-70) cc_final: 0.4915 (p90) REVERT: B 197 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.5860 (m-80) REVERT: B 207 MET cc_start: -0.0116 (tpt) cc_final: -0.0433 (ttp) REVERT: C 138 GLN cc_start: 0.6288 (tp40) cc_final: 0.4992 (pt0) REVERT: C 171 PHE cc_start: 0.7225 (t80) cc_final: 0.5601 (p90) REVERT: C 192 MET cc_start: 0.5721 (tpt) cc_final: 0.5293 (tpt) REVERT: C 197 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6232 (m-80) REVERT: C 207 MET cc_start: 0.0002 (tpt) cc_final: -0.0526 (ptm) REVERT: C 219 ILE cc_start: 0.6204 (mm) cc_final: 0.5381 (mm) REVERT: C 223 ASN cc_start: 0.5733 (OUTLIER) cc_final: 0.5378 (p0) outliers start: 24 outliers final: 1 residues processed: 72 average time/residue: 0.1194 time to fit residues: 11.0974 Evaluate side-chains 45 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 0.0770 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- 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 170 GLN ** 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 222 HIS B 245 GLN ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 HIS C 229 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN C 245 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5629 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3516 Z= 0.286 Angle : 0.815 8.540 4788 Z= 0.426 Chirality : 0.061 0.293 606 Planarity : 0.004 0.037 579 Dihedral : 13.434 103.928 711 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 239 PHE 0.018 0.003 PHE A 171 TYR 0.018 0.003 TYR A 143 ARG 0.003 0.001 ARG C 247 *********************** 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 52 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.372 Fit side-chains REVERT: A 226 LEU cc_start: 0.5339 (mt) cc_final: 0.5134 (mt) REVERT: B 223 ASN cc_start: 0.7522 (t0) cc_final: 0.7172 (t0) REVERT: C 192 MET cc_start: 0.6249 (tpt) cc_final: 0.5984 (tpt) REVERT: C 223 ASN cc_start: 0.6853 (t0) cc_final: 0.6470 (t0) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1115 time to fit residues: 7.7798 Evaluate side-chains 40 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 40.0000 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3516 Z= 0.312 Angle : 0.869 8.142 4788 Z= 0.454 Chirality : 0.063 0.390 606 Planarity : 0.004 0.036 579 Dihedral : 14.326 108.772 711 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % 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: -3.59 (0.37), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 239 PHE 0.021 0.003 PHE A 171 TYR 0.020 0.003 TYR C 143 ARG 0.002 0.000 ARG B 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 51 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: B 186 ILE cc_start: 0.8034 (tt) cc_final: 0.7822 (mp) REVERT: B 192 MET cc_start: 0.6476 (tpt) cc_final: 0.6197 (tpt) REVERT: B 230 VAL cc_start: 0.7692 (t) cc_final: 0.7492 (p) REVERT: C 140 ARG cc_start: 0.7111 (tpt90) cc_final: 0.5261 (tmt170) REVERT: C 192 MET cc_start: 0.6274 (tpt) cc_final: 0.5452 (tpt) REVERT: C 223 ASN cc_start: 0.7627 (t0) cc_final: 0.7315 (t0) REVERT: C 250 TYR cc_start: 0.7262 (t80) cc_final: 0.5667 (p90) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1278 time to fit residues: 8.4478 Evaluate side-chains 41 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3516 Z= 0.280 Angle : 0.835 8.413 4788 Z= 0.432 Chirality : 0.062 0.369 606 Planarity : 0.004 0.032 579 Dihedral : 14.369 109.144 711 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: -3.59 (0.37), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS A 239 PHE 0.019 0.003 PHE A 171 TYR 0.017 0.003 TYR B 157 ARG 0.002 0.000 ARG B 140 *********************** 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 49 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.337 Fit side-chains REVERT: B 186 ILE cc_start: 0.8040 (tt) cc_final: 0.7712 (mp) REVERT: B 192 MET cc_start: 0.6908 (tpt) cc_final: 0.6592 (tpt) REVERT: C 192 MET cc_start: 0.6378 (tpt) cc_final: 0.5790 (tpp) REVERT: C 219 ILE cc_start: 0.6850 (mm) cc_final: 0.6632 (mt) REVERT: C 223 ASN cc_start: 0.7447 (t0) cc_final: 0.7189 (t0) REVERT: C 250 TYR cc_start: 0.7760 (t80) cc_final: 0.5664 (p90) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0924 time to fit residues: 6.5106 Evaluate side-chains 39 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 170 GLN ** 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 ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.7193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3516 Z= 0.310 Angle : 0.895 9.026 4788 Z= 0.457 Chirality : 0.064 0.421 606 Planarity : 0.004 0.031 579 Dihedral : 14.917 109.626 711 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: -3.84 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 239 PHE 0.021 0.003 PHE A 171 TYR 0.020 0.003 TYR A 143 ARG 0.001 0.000 ARG B 247 *********************** 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 47 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.378 Fit side-chains REVERT: A 224 ILE cc_start: 0.8142 (mm) cc_final: 0.7940 (mm) REVERT: B 186 ILE cc_start: 0.8132 (tt) cc_final: 0.7716 (mp) REVERT: B 192 MET cc_start: 0.7105 (tpt) cc_final: 0.6605 (tpt) REVERT: C 228 MET cc_start: 0.6392 (ppp) cc_final: 0.5775 (ptm) REVERT: C 250 TYR cc_start: 0.7577 (t80) cc_final: 0.5554 (p90) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0951 time to fit residues: 6.3431 Evaluate side-chains 38 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 170 GLN ** 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 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.7715 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= 0.337 Angle : 0.948 10.621 4788 Z= 0.486 Chirality : 0.068 0.506 606 Planarity : 0.004 0.028 579 Dihedral : 14.784 109.641 711 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.89 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 239 PHE 0.030 0.004 PHE A 237 TYR 0.022 0.004 TYR B 157 ARG 0.002 0.000 ARG B 247 *********************** 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 52 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.410 Fit side-chains REVERT: B 192 MET cc_start: 0.7013 (tpt) cc_final: 0.5757 (tpt) REVERT: C 186 ILE cc_start: 0.7785 (mp) cc_final: 0.7533 (mt) REVERT: C 250 TYR cc_start: 0.7931 (t80) cc_final: 0.5858 (p90) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0917 time to fit residues: 6.7487 Evaluate side-chains 41 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- 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 155 ASN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.8054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3516 Z= 0.318 Angle : 0.899 9.805 4788 Z= 0.462 Chirality : 0.065 0.441 606 Planarity : 0.004 0.027 579 Dihedral : 14.783 109.241 711 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.79 % Favored : 85.21 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.00 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS C 239 PHE 0.023 0.004 PHE A 237 TYR 0.022 0.004 TYR B 157 ARG 0.001 0.000 ARG B 247 *********************** 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 44 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.421 Fit side-chains REVERT: B 192 MET cc_start: 0.6647 (tpt) cc_final: 0.5955 (tpt) REVERT: B 226 LEU cc_start: 0.6227 (mp) cc_final: 0.5926 (mp) REVERT: B 250 TYR cc_start: 0.7677 (t80) cc_final: 0.7327 (t80) REVERT: C 186 ILE cc_start: 0.7789 (mp) cc_final: 0.7547 (mt) REVERT: C 228 MET cc_start: 0.6367 (ptm) cc_final: 0.6153 (ppp) REVERT: C 250 TYR cc_start: 0.8009 (t80) cc_final: 0.5807 (p90) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0981 time to fit residues: 6.0665 Evaluate side-chains 37 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 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 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** 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 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.8323 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= 0.327 Angle : 0.921 10.436 4788 Z= 0.471 Chirality : 0.065 0.434 606 Planarity : 0.004 0.025 579 Dihedral : 14.938 108.160 711 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.29 % Favored : 84.71 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.12 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 239 PHE 0.028 0.004 PHE A 237 TYR 0.021 0.004 TYR B 157 ARG 0.002 0.000 ARG B 247 *********************** 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 44 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.387 Fit side-chains REVERT: A 195 ILE cc_start: 0.8776 (pt) cc_final: 0.8265 (mp) REVERT: B 192 MET cc_start: 0.6524 (tpt) cc_final: 0.5960 (tpt) REVERT: B 217 ILE cc_start: 0.7558 (mp) cc_final: 0.7338 (mt) REVERT: C 186 ILE cc_start: 0.7782 (mp) cc_final: 0.7555 (mt) REVERT: C 250 TYR cc_start: 0.8055 (t80) cc_final: 0.5747 (p90) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0959 time to fit residues: 6.0406 Evaluate side-chains 38 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 30 optimal weight: 0.0870 chunk 3 optimal weight: 7.9990 overall best weight: 3.1964 ------------------------------------------------------------------------------- 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 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** 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 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.8333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3516 Z= 0.260 Angle : 0.827 10.865 4788 Z= 0.424 Chirality : 0.060 0.338 606 Planarity : 0.004 0.023 579 Dihedral : 14.629 107.759 711 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -4.01 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 239 PHE 0.017 0.003 PHE A 237 TYR 0.018 0.003 TYR C 125 ARG 0.001 0.000 ARG B 247 *********************** 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 41 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.387 Fit side-chains REVERT: B 192 MET cc_start: 0.6699 (tpt) cc_final: 0.6360 (tpt) REVERT: C 186 ILE cc_start: 0.7796 (mp) cc_final: 0.7584 (mt) REVERT: C 250 TYR cc_start: 0.8083 (t80) cc_final: 0.5813 (p90) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0942 time to fit residues: 5.5637 Evaluate side-chains 36 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.8746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 3516 Z= 0.395 Angle : 1.009 11.723 4788 Z= 0.521 Chirality : 0.068 0.489 606 Planarity : 0.005 0.033 579 Dihedral : 15.070 105.665 711 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.30 % Favored : 81.70 % Rotamer: Outliers : 0.26 % Allowed : 0.52 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.25 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS C 239 PHE 0.032 0.005 PHE A 237 TYR 0.026 0.005 TYR C 125 ARG 0.002 0.000 ARG B 247 ********************** 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 44 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.7240 (tpt) cc_final: 0.6261 (tpt) REVERT: B 217 ILE cc_start: 0.7517 (mp) cc_final: 0.7269 (mt) REVERT: C 250 TYR cc_start: 0.8178 (t80) cc_final: 0.5828 (p90) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.0964 time to fit residues: 6.0213 Evaluate side-chains 36 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 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** ** A 170 GLN ** 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 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.272082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.202366 restraints weight = 17488.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.194255 restraints weight = 20064.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.193509 restraints weight = 16997.465| |-----------------------------------------------------------------------------| r_work (final): 0.4829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4829 r_free = 0.4829 target_work(ls_wunit_k1) = 0.247 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4829 r_free = 0.4829 target_work(ls_wunit_k1) = 0.247 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.8865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3516 Z= 0.359 Angle : 0.961 10.924 4788 Z= 0.497 Chirality : 0.066 0.453 606 Planarity : 0.005 0.028 579 Dihedral : 15.002 105.578 711 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.54 % Favored : 84.46 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.28 (0.34), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 239 PHE 0.030 0.004 PHE A 237 TYR 0.023 0.004 TYR B 157 ARG 0.002 0.000 ARG B 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 953.93 seconds wall clock time: 18 minutes 15.51 seconds (1095.51 seconds total)