Starting phenix.real_space_refine on Sun Mar 10 17:09:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u10_26273/03_2024/7u10_26273.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u10_26273/03_2024/7u10_26273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u10_26273/03_2024/7u10_26273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u10_26273/03_2024/7u10_26273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u10_26273/03_2024/7u10_26273.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u10_26273/03_2024/7u10_26273.pdb" } resolution = 3.0 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 21 5.16 5 C 2178 2.51 5 N 531 2.21 5 O 699 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 3429 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "B" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "C" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 2.37, per 1000 atoms: 0.69 Number of scatterers: 3429 At special positions: 0 Unit cell: (105.252, 98.808, 32.22, 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 699 8.00 N 531 7.00 C 2178 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=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 301 " - " ASN A 183 " " NAG A 302 " - " ASN A 151 " " NAG A 303 " - " ASN A 145 " " NAG A 304 " - " ASN A 164 " " NAG B 301 " - " ASN B 183 " " NAG B 302 " - " ASN B 151 " " NAG B 303 " - " ASN B 145 " " NAG B 304 " - " ASN B 164 " " NAG C 301 " - " ASN C 183 " " NAG C 302 " - " ASN C 151 " " NAG C 303 " - " ASN C 145 " " NAG C 304 " - " ASN C 164 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 571.3 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 63.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 126 removed outlier: 6.501A pdb=" N VAL A 123 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE B 126 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR A 125 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 123 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE C 126 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR B 125 " --> pdb=" O ILE C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 137 removed outlier: 6.396A pdb=" N LYS A 129 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N TYR B 132 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N ALA A 131 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER B 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N VAL A 133 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N ASP B 136 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N TYR A 135 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N TYR C 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N ALA B 131 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER C 134 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N VAL B 133 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N ASP C 136 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 8.715A 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 142 through 160 removed outlier: 6.993A pdb=" N ILE A 146 " --> pdb=" O ASN B 145 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR B 147 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASN A 148 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N THR B 149 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A 150 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASN B 151 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE A 152 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR B 153 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN A 154 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN B 155 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN A 156 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR B 157 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR A 158 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SER B 159 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL A 160 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE B 146 " --> pdb=" O ASN C 145 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR C 147 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 6.996A 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: 6.979A pdb=" N LEU B 150 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASN C 151 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE B 152 " --> pdb=" O ASN C 151 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C 153 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN B 154 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN C 155 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ASN B 156 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR C 157 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR B 158 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER C 159 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 160 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 165 removed outlier: 6.047A pdb=" N ASN B 164 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 168 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.633A pdb=" N ARG A 180 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG B 180 " --> pdb=" O LEU C 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 185 through 187 removed outlier: 6.503A pdb=" N THR A 185 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 191 through 198 removed outlier: 8.916A pdb=" N MET A 192 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ILE B 195 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLN A 194 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N TYR B 197 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP A 196 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N MET B 192 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N ILE C 195 " --> pdb=" O MET B 192 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN B 194 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N TYR C 197 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 196 " --> pdb=" O TYR C 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 201 through 204 removed outlier: 6.382A pdb=" N VAL A 202 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 202 " --> pdb=" O ILE C 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 209 through 228 removed outlier: 6.131A pdb=" N TYR A 209 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP B 212 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR A 211 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS B 214 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N PHE A 213 " --> pdb=" O CYS B 214 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N LEU B 216 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N THR A 215 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N SER B 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N ILE A 217 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N LYS B 220 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE A 219 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N HIS B 222 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL A 221 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE B 224 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ASN A 223 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N LEU B 226 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL A 225 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N MET B 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N MET A 227 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR B 209 " --> pdb=" O MET C 210 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASP C 212 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR B 211 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N CYS C 214 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N PHE B 213 " --> pdb=" O CYS C 214 " (cutoff:3.500A) removed outlier: 10.587A pdb=" N LEU C 216 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N THR B 215 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N SER C 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N ILE B 217 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 10.142A pdb=" N LYS C 220 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE B 219 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N HIS C 222 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL B 221 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE C 224 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASN B 223 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N LEU C 226 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N VAL B 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 10.369A pdb=" N MET C 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N MET B 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 233 through 243 Processing sheet with id=AB3, first strand: chain 'A' and resid 246 through 249 54 hydrogen bonds defined for protein. 162 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: 0.79 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1053 1.34 - 1.46: 816 1.46 - 1.58: 1578 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 3483 Sorted by residual: bond pdb=" C1 NAG C 304 " pdb=" O5 NAG C 304 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C1 NAG B 304 " pdb=" O5 NAG B 304 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1 NAG A 304 " pdb=" O5 NAG A 304 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 NAG C 303 " pdb=" O5 NAG C 303 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" C1 NAG B 303 " pdb=" O5 NAG B 303 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.17e+00 ... (remaining 3478 not shown) Histogram of bond angle deviations from ideal: 100.65 - 106.77: 70 106.77 - 112.90: 1962 112.90 - 119.02: 869 119.02 - 125.15: 1824 125.15 - 131.27: 12 Bond angle restraints: 4737 Sorted by residual: angle pdb=" CG1 VAL C 230 " pdb=" CB VAL C 230 " pdb=" CG2 VAL C 230 " ideal model delta sigma weight residual 110.80 106.40 4.40 2.20e+00 2.07e-01 4.00e+00 angle pdb=" CG1 VAL B 230 " pdb=" CB VAL B 230 " pdb=" CG2 VAL B 230 " ideal model delta sigma weight residual 110.80 106.45 4.35 2.20e+00 2.07e-01 3.91e+00 angle pdb=" CG1 VAL A 230 " pdb=" CB VAL A 230 " pdb=" CG2 VAL A 230 " ideal model delta sigma weight residual 110.80 106.47 4.33 2.20e+00 2.07e-01 3.87e+00 angle pdb=" CA GLN C 245 " pdb=" CB GLN C 245 " pdb=" CG GLN C 245 " ideal model delta sigma weight residual 114.10 117.79 -3.69 2.00e+00 2.50e-01 3.41e+00 angle pdb=" CA GLN A 245 " pdb=" CB GLN A 245 " pdb=" CG GLN A 245 " ideal model delta sigma weight residual 114.10 117.77 -3.67 2.00e+00 2.50e-01 3.36e+00 ... (remaining 4732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.75: 2088 24.75 - 49.51: 126 49.51 - 74.26: 21 74.26 - 99.01: 12 99.01 - 123.76: 3 Dihedral angle restraints: 2250 sinusoidal: 1032 harmonic: 1218 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 -86.00 -31.95 -54.05 1 1.00e+01 1.00e-02 3.96e+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 -86.00 -32.05 -53.95 1 1.00e+01 1.00e-02 3.95e+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 -86.00 -32.07 -53.93 1 1.00e+01 1.00e-02 3.95e+01 ... (remaining 2247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 354 0.036 - 0.072: 147 0.072 - 0.108: 58 0.108 - 0.144: 38 0.144 - 0.180: 6 Chirality restraints: 603 Sorted by residual: chirality pdb=" C1 NAG C 301 " pdb=" ND2 ASN C 183 " pdb=" C2 NAG C 301 " pdb=" O5 NAG C 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" C1 NAG A 301 " pdb=" ND2 ASN A 183 " pdb=" C2 NAG A 301 " pdb=" O5 NAG A 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" C1 NAG B 301 " pdb=" ND2 ASN B 183 " pdb=" C2 NAG B 301 " pdb=" O5 NAG B 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 600 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 158 " 0.003 2.00e-02 2.50e+03 1.31e-02 3.43e+00 pdb=" CG TYR A 158 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 158 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 158 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 158 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 158 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 158 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 158 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 158 " 0.003 2.00e-02 2.50e+03 1.29e-02 3.32e+00 pdb=" CG TYR B 158 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 158 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 158 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 158 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 158 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 158 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 158 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 158 " 0.003 2.00e-02 2.50e+03 1.28e-02 3.27e+00 pdb=" CG TYR C 158 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR C 158 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR C 158 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR C 158 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 158 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 158 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 158 " -0.001 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 286 2.76 - 3.30: 3209 3.30 - 3.83: 5871 3.83 - 4.37: 6193 4.37 - 4.90: 12302 Nonbonded interactions: 27861 Sorted by model distance: nonbonded pdb=" OE1 GLN C 229 " pdb=" OG1 THR C 234 " model vdw 2.230 2.440 nonbonded pdb=" OE1 GLN B 229 " pdb=" OG1 THR B 234 " model vdw 2.230 2.440 nonbonded pdb=" OE1 GLN A 229 " pdb=" OG1 THR A 234 " model vdw 2.230 2.440 nonbonded pdb=" N SER B 120 " pdb=" OE1 GLU C 241 " model vdw 2.261 2.520 nonbonded pdb=" NZ LYS B 129 " pdb=" OD2 ASP B 136 " model vdw 2.271 2.520 ... (remaining 27856 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.970 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 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 : 0.004 0.071 3483 Z= 0.254 Angle : 0.638 4.398 4737 Z= 0.330 Chirality : 0.053 0.180 603 Planarity : 0.002 0.013 573 Dihedral : 17.217 123.763 1461 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: -2.82 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 222 PHE 0.013 0.002 PHE A 213 TYR 0.027 0.002 TYR A 158 ARG 0.001 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: B 234 THR cc_start: 0.7622 (t) cc_final: 0.7406 (t) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.6496 time to fit residues: 52.8225 Evaluate side-chains 49 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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: 4.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 168 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN C 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3483 Z= 0.380 Angle : 0.768 7.191 4737 Z= 0.409 Chirality : 0.062 0.452 603 Planarity : 0.004 0.033 573 Dihedral : 16.743 118.648 702 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.82 % Allowed : 15.08 % Favored : 79.10 % 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: -3.24 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 239 PHE 0.015 0.003 PHE C 237 TYR 0.022 0.004 TYR B 158 ARG 0.002 0.001 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 46 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 TYR cc_start: 0.6083 (OUTLIER) cc_final: 0.5667 (m-10) REVERT: C 135 TYR cc_start: 0.6388 (OUTLIER) cc_final: 0.5523 (m-10) REVERT: C 183 ASN cc_start: 0.5516 (m110) cc_final: 0.5221 (p0) outliers start: 22 outliers final: 8 residues processed: 61 average time/residue: 0.7716 time to fit residues: 49.2520 Evaluate side-chains 49 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN B 170 GLN C 168 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3483 Z= 0.247 Angle : 0.634 6.691 4737 Z= 0.334 Chirality : 0.057 0.380 603 Planarity : 0.002 0.012 573 Dihedral : 16.460 114.029 702 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.50 % Allowed : 20.11 % Favored : 75.40 % 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: -3.25 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 239 PHE 0.007 0.002 PHE C 171 TYR 0.013 0.002 TYR A 143 ARG 0.001 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.5663 (m-10) outliers start: 17 outliers final: 8 residues processed: 57 average time/residue: 0.6723 time to fit residues: 40.3992 Evaluate side-chains 45 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN C 168 GLN C 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3483 Z= 0.414 Angle : 0.784 7.207 4737 Z= 0.417 Chirality : 0.064 0.464 603 Planarity : 0.004 0.036 573 Dihedral : 16.840 117.226 702 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 6.35 % Allowed : 21.69 % Favored : 71.96 % 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: -3.54 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 239 PHE 0.013 0.002 PHE C 171 TYR 0.025 0.004 TYR A 143 ARG 0.003 0.001 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 35 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 TYR cc_start: 0.6424 (OUTLIER) cc_final: 0.5862 (m-10) REVERT: C 135 TYR cc_start: 0.6447 (OUTLIER) cc_final: 0.5756 (m-10) REVERT: C 183 ASN cc_start: 0.5972 (m110) cc_final: 0.5714 (p0) outliers start: 24 outliers final: 13 residues processed: 52 average time/residue: 0.7805 time to fit residues: 42.5657 Evaluate side-chains 47 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 32 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 33 optimal weight: 0.0070 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 GLN ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3483 Z= 0.182 Angle : 0.638 7.647 4737 Z= 0.327 Chirality : 0.059 0.375 603 Planarity : 0.002 0.015 573 Dihedral : 16.111 116.600 702 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.97 % Allowed : 23.28 % Favored : 72.75 % 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: -3.33 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 239 PHE 0.006 0.001 PHE C 237 TYR 0.016 0.002 TYR A 143 ARG 0.001 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 42 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 51 average time/residue: 0.7051 time to fit residues: 37.8992 Evaluate side-chains 42 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN C 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 3483 Z= 0.484 Angle : 0.854 8.441 4737 Z= 0.450 Chirality : 0.067 0.484 603 Planarity : 0.004 0.036 573 Dihedral : 16.742 119.843 702 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 5.56 % Allowed : 24.07 % Favored : 70.37 % 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: -3.72 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 239 PHE 0.016 0.003 PHE C 171 TYR 0.022 0.004 TYR C 125 ARG 0.002 0.001 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 38 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.6468 (OUTLIER) cc_final: 0.6254 (m-10) REVERT: B 234 THR cc_start: 0.8028 (t) cc_final: 0.7767 (t) REVERT: C 135 TYR cc_start: 0.6828 (OUTLIER) cc_final: 0.6619 (m-10) REVERT: C 183 ASN cc_start: 0.6387 (m110) cc_final: 0.5976 (p0) REVERT: C 213 PHE cc_start: 0.6959 (m-10) cc_final: 0.6490 (p90) outliers start: 21 outliers final: 11 residues processed: 54 average time/residue: 0.7514 time to fit residues: 42.6440 Evaluate side-chains 47 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 34 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3483 Z= 0.210 Angle : 0.697 8.718 4737 Z= 0.353 Chirality : 0.059 0.377 603 Planarity : 0.002 0.018 573 Dihedral : 15.866 116.041 702 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.44 % Allowed : 27.51 % Favored : 69.05 % 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: -3.58 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 239 PHE 0.005 0.001 PHE B 171 TYR 0.013 0.002 TYR B 248 ARG 0.001 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 PHE cc_start: 0.6837 (m-10) cc_final: 0.6452 (p90) outliers start: 13 outliers final: 8 residues processed: 49 average time/residue: 0.7578 time to fit residues: 39.0182 Evaluate side-chains 44 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3483 Z= 0.188 Angle : 0.665 9.396 4737 Z= 0.339 Chirality : 0.058 0.326 603 Planarity : 0.002 0.019 573 Dihedral : 15.628 114.443 702 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.17 % Allowed : 26.98 % Favored : 69.84 % 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: -3.47 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 239 PHE 0.005 0.001 PHE B 171 TYR 0.013 0.001 TYR A 143 ARG 0.001 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 PHE cc_start: 0.6796 (m-10) cc_final: 0.6466 (p90) outliers start: 12 outliers final: 9 residues processed: 48 average time/residue: 0.6403 time to fit residues: 32.6921 Evaluate side-chains 43 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3483 Z= 0.202 Angle : 0.667 9.622 4737 Z= 0.341 Chirality : 0.059 0.334 603 Planarity : 0.003 0.031 573 Dihedral : 15.358 113.353 702 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.70 % Allowed : 26.46 % Favored : 69.84 % 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: -3.42 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 239 PHE 0.005 0.001 PHE B 171 TYR 0.013 0.002 TYR C 143 ARG 0.001 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 34 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 PHE cc_start: 0.6805 (m-10) cc_final: 0.6485 (p90) outliers start: 14 outliers final: 10 residues processed: 46 average time/residue: 0.6894 time to fit residues: 33.8499 Evaluate side-chains 43 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN B 168 GLN C 156 ASN C 170 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3483 Z= 0.500 Angle : 0.874 10.133 4737 Z= 0.460 Chirality : 0.067 0.456 603 Planarity : 0.004 0.032 573 Dihedral : 16.716 116.738 702 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 2.91 % Allowed : 28.31 % Favored : 68.78 % 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: -3.80 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 222 PHE 0.013 0.003 PHE C 171 TYR 0.029 0.005 TYR A 125 ARG 0.003 0.000 ARG A 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.6631 (m-80) REVERT: C 183 ASN cc_start: 0.6355 (m110) cc_final: 0.5997 (p0) REVERT: C 213 PHE cc_start: 0.6956 (m-10) cc_final: 0.6559 (p90) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.8016 time to fit residues: 39.5496 Evaluate side-chains 46 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN B 168 GLN C 156 ASN ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5873 r_free = 0.5873 target = 0.452911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.6797 r_free = 0.6797 target = 0.374627 restraints weight = 5298.075| |-----------------------------------------------------------------------------| r_work (start): 0.5198 rms_B_bonded: 1.09 r_work: 0.5107 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.5044 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.5044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3483 Z= 0.199 Angle : 0.700 10.311 4737 Z= 0.358 Chirality : 0.060 0.348 603 Planarity : 0.003 0.031 573 Dihedral : 15.947 115.044 702 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.65 % Allowed : 29.37 % Favored : 67.99 % 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: -3.66 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 239 PHE 0.007 0.001 PHE B 171 TYR 0.014 0.002 TYR B 248 ARG 0.001 0.000 ARG A 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1485.70 seconds wall clock time: 27 minutes 22.55 seconds (1642.55 seconds total)