Starting phenix.real_space_refine on Sun Mar 10 17:18:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u12_26275/03_2024/7u12_26275.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u12_26275/03_2024/7u12_26275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u12_26275/03_2024/7u12_26275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u12_26275/03_2024/7u12_26275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u12_26275/03_2024/7u12_26275.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u12_26275/03_2024/7u12_26275.pdb" } resolution = 3.5 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= 0.002 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 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 "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3.67, per 1000 atoms: 1.06 Number of scatterers: 3456 At special positions: 0 Unit cell: (98.808, 118.14, 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 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: 1.25 Conformation dependent library (CDL) restraints added in 1.2 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, 64.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 125 removed outlier: 6.633A pdb=" N VAL A 123 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 123 " --> pdb=" O LYS C 124 " (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: 9.036A pdb=" N SER A 130 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N VAL B 133 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N TYR A 132 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N TYR B 135 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER A 134 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL B 137 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP A 136 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N SER B 130 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 9.429A pdb=" N VAL C 133 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR B 132 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N TYR C 135 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER B 134 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL C 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP B 136 " --> pdb=" O VAL C 137 " (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: 5.950A pdb=" N ILE A 142 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASN B 145 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N LEU A 144 " --> pdb=" O ASN B 145 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR B 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N ILE A 146 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N THR B 149 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N ASN A 148 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N ASN B 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N LEU A 150 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N THR B 153 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N ILE A 152 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N ASN B 155 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ASN A 154 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N TYR B 157 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N ASN A 156 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N SER B 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N TYR A 158 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N GLU B 161 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL A 160 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLU B 163 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A 162 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE B 165 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ASN A 164 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE B 142 " --> pdb=" O TYR C 143 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN C 145 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N LEU B 144 " --> pdb=" O ASN C 145 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR C 147 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N ILE B 146 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N THR C 149 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ASN B 148 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N ASN C 151 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N LEU B 150 " --> pdb=" O ASN C 151 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N THR C 153 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N ILE B 152 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N ASN C 155 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N ASN B 154 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 10.542A pdb=" N TYR C 157 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N ASN B 156 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N SER C 159 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N TYR B 158 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 10.323A pdb=" N GLU C 161 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL B 160 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N GLU C 163 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 162 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE C 165 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASN B 164 " --> pdb=" O ILE C 165 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 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: 6.568A 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 Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 198 removed outlier: 8.946A pdb=" N MET A 192 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N ILE B 195 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN A 194 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N TYR B 197 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP A 196 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N MET B 192 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N ILE C 195 " --> pdb=" O MET B 192 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN B 194 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N TYR C 197 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 196 " --> pdb=" O TYR C 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.452A pdb=" N VAL A 202 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.502A 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: 6.952A 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: 6.974A pdb=" N ASP A 212 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE B 213 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N MET B 210 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TYR C 211 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP B 212 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE C 213 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 222 through 228 removed outlier: 6.991A pdb=" N HIS A 222 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL B 225 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 224 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N MET B 227 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 226 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N HIS B 222 " --> pdb=" O ASN C 223 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N VAL C 225 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 224 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N MET C 227 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 226 " --> pdb=" O MET C 227 " (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 245 removed outlier: 6.422A pdb=" N THR A 234 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N PHE B 237 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR A 236 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N HIS B 239 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 238 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N GLU B 241 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER A 240 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE B 243 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN A 242 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLN B 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N SER A 244 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR B 234 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N PHE C 237 " --> pdb=" O THR B 234 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR B 236 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N HIS C 239 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY B 238 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLU C 241 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER B 240 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE C 243 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN B 242 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLN C 245 " --> pdb=" O GLN B 242 " (cutoff:3.500A) removed outlier: 6.118A 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 removed outlier: 6.309A pdb=" N VAL A 251 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 251 " --> pdb=" O ASP C 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 36 hydrogen bonds defined for protein. 108 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: 0.73 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1051 1.34 - 1.46: 685 1.46 - 1.57: 1741 1.57 - 1.69: 3 1.69 - 1.81: 36 Bond restraints: 3516 Sorted by residual: bond pdb=" CG PRO C 189 " pdb=" CD PRO C 189 " ideal model delta sigma weight residual 1.503 1.253 0.250 3.40e-02 8.65e+02 5.40e+01 bond pdb=" CG PRO A 189 " pdb=" CD PRO A 189 " ideal model delta sigma weight residual 1.503 1.253 0.250 3.40e-02 8.65e+02 5.39e+01 bond pdb=" CG PRO B 189 " pdb=" CD PRO B 189 " ideal model delta sigma weight residual 1.503 1.255 0.248 3.40e-02 8.65e+02 5.34e+01 bond pdb=" CB PRO B 189 " pdb=" CG PRO B 189 " ideal model delta sigma weight residual 1.492 1.669 -0.177 5.00e-02 4.00e+02 1.26e+01 bond pdb=" CB PRO C 189 " pdb=" CG PRO C 189 " ideal model delta sigma weight residual 1.492 1.669 -0.177 5.00e-02 4.00e+02 1.25e+01 ... (remaining 3511 not shown) Histogram of bond angle deviations from ideal: 89.32 - 97.76: 6 97.76 - 106.19: 56 106.19 - 114.63: 2146 114.63 - 123.07: 2200 123.07 - 131.51: 380 Bond angle restraints: 4788 Sorted by residual: angle pdb=" N PRO C 189 " pdb=" CD PRO C 189 " pdb=" CG PRO C 189 " ideal model delta sigma weight residual 103.20 89.32 13.88 1.50e+00 4.44e-01 8.56e+01 angle pdb=" N PRO A 189 " pdb=" CD PRO A 189 " pdb=" CG PRO A 189 " ideal model delta sigma weight residual 103.20 89.34 13.86 1.50e+00 4.44e-01 8.53e+01 angle pdb=" N PRO B 189 " pdb=" CD PRO B 189 " pdb=" CG PRO B 189 " ideal model delta sigma weight residual 103.20 89.37 13.83 1.50e+00 4.44e-01 8.50e+01 angle pdb=" N PHE A 171 " pdb=" CA PHE A 171 " pdb=" C PHE A 171 " ideal model delta sigma weight residual 108.96 115.81 -6.85 1.49e+00 4.50e-01 2.12e+01 angle pdb=" N PHE B 171 " pdb=" CA PHE B 171 " pdb=" C PHE B 171 " ideal model delta sigma weight residual 108.96 115.78 -6.82 1.49e+00 4.50e-01 2.10e+01 ... (remaining 4783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 1965 16.69 - 33.37: 189 33.37 - 50.06: 91 50.06 - 66.74: 17 66.74 - 83.43: 9 Dihedral angle restraints: 2271 sinusoidal: 1038 harmonic: 1233 Sorted by residual: 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 30.37 62.63 1 1.00e+01 1.00e-02 5.19e+01 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 30.37 62.63 1 1.00e+01 1.00e-02 5.19e+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 30.42 62.58 1 1.00e+01 1.00e-02 5.18e+01 ... (remaining 2268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 474 0.081 - 0.162: 111 0.162 - 0.243: 15 0.243 - 0.324: 3 0.324 - 0.405: 3 Chirality restraints: 606 Sorted by residual: chirality pdb=" CG LEU A 226 " pdb=" CB LEU A 226 " pdb=" CD1 LEU A 226 " pdb=" CD2 LEU A 226 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CG LEU B 226 " pdb=" CB LEU B 226 " pdb=" CD1 LEU B 226 " pdb=" CD2 LEU B 226 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CG LEU C 226 " pdb=" CB LEU C 226 " pdb=" CD1 LEU C 226 " pdb=" CD2 LEU C 226 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.39 2.00e-01 2.50e+01 3.90e+00 ... (remaining 603 not shown) Planarity restraints: 591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 125 " -0.004 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR A 125 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 125 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 125 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A 125 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 125 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 125 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 125 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 125 " -0.005 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR C 125 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR C 125 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR C 125 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR C 125 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR C 125 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR C 125 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 125 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 125 " -0.004 2.00e-02 2.50e+03 2.39e-02 1.15e+01 pdb=" CG TYR B 125 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 125 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR B 125 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B 125 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 125 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 125 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 125 " 0.007 2.00e-02 2.50e+03 ... (remaining 588 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 86 2.71 - 3.26: 3290 3.26 - 3.80: 5387 3.80 - 4.35: 6630 4.35 - 4.90: 12470 Nonbonded interactions: 27863 Sorted by model distance: nonbonded pdb=" OG1 THR A 215 " pdb=" OD1 ASP B 212 " model vdw 2.160 2.440 nonbonded pdb=" OG1 THR B 215 " pdb=" OD1 ASP C 212 " model vdw 2.214 2.440 nonbonded pdb=" NZ LYS A 129 " pdb=" OD2 ASP A 136 " model vdw 2.277 2.520 nonbonded pdb=" NZ LYS C 129 " pdb=" OD2 ASP C 136 " model vdw 2.279 2.520 nonbonded pdb=" NZ LYS B 129 " pdb=" OD2 ASP B 136 " model vdw 2.279 2.520 ... (remaining 27858 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.020 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.770 Find NCS groups from input model: 0.200 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4439 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 : 0.011 0.250 3516 Z= 0.746 Angle : 1.061 13.880 4788 Z= 0.607 Chirality : 0.072 0.405 606 Planarity : 0.008 0.081 579 Dihedral : 16.716 83.426 1476 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 5.51 % Allowed : 2.36 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.37), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 239 PHE 0.045 0.007 PHE B 171 TYR 0.050 0.004 TYR C 125 ARG 0.008 0.002 ARG B 140 *********************** 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 130 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 0.398 Fit side-chains REVERT: A 178 LYS cc_start: 0.4567 (OUTLIER) cc_final: 0.3467 (mmpt) REVERT: C 178 LYS cc_start: 0.4744 (OUTLIER) cc_final: 0.4489 (pptt) REVERT: C 207 MET cc_start: 0.3545 (tmm) cc_final: 0.3187 (tmm) outliers start: 21 outliers final: 0 residues processed: 113 average time/residue: 0.1484 time to fit residues: 20.4559 Evaluate side-chains 73 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain C residue 178 LYS 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: 9.9990 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 245 GLN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5195 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 3516 Z= 0.359 Angle : 0.884 7.481 4788 Z= 0.475 Chirality : 0.061 0.420 606 Planarity : 0.005 0.033 579 Dihedral : 8.141 40.222 719 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.46 % Allowed : 11.81 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.34), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 239 PHE 0.013 0.002 PHE B 237 TYR 0.024 0.003 TYR B 132 ARG 0.004 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 205 GLU cc_start: 0.6082 (mm-30) cc_final: 0.5775 (pm20) REVERT: C 172 SER cc_start: 0.7585 (t) cc_final: 0.7229 (m) REVERT: C 207 MET cc_start: 0.4457 (tmm) cc_final: 0.3785 (tmm) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.1194 time to fit residues: 15.8372 Evaluate side-chains 91 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 244 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.0670 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 0.0670 chunk 31 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5149 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3516 Z= 0.197 Angle : 0.680 8.082 4788 Z= 0.361 Chirality : 0.056 0.315 606 Planarity : 0.003 0.027 579 Dihedral : 7.050 40.220 711 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.89 % Allowed : 17.32 % Favored : 79.79 % 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: -3.38 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 239 PHE 0.008 0.002 PHE B 237 TYR 0.011 0.001 TYR B 250 ARG 0.002 0.000 ARG C 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 99 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.394 Fit side-chains REVERT: A 213 PHE cc_start: 0.6031 (t80) cc_final: 0.5805 (t80) REVERT: A 216 LEU cc_start: 0.7483 (mp) cc_final: 0.7210 (tt) REVERT: C 172 SER cc_start: 0.7694 (t) cc_final: 0.7354 (m) outliers start: 11 outliers final: 9 residues processed: 93 average time/residue: 0.1081 time to fit residues: 13.0942 Evaluate side-chains 87 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR 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: 9.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 0.0070 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 6.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5573 moved from start: 0.8975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 3516 Z= 0.438 Angle : 0.962 12.088 4788 Z= 0.512 Chirality : 0.067 0.470 606 Planarity : 0.004 0.027 579 Dihedral : 9.872 44.607 711 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 5.25 % Allowed : 18.64 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 239 PHE 0.018 0.003 PHE B 237 TYR 0.024 0.004 TYR C 158 ARG 0.004 0.001 ARG A 180 *********************** 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 104 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.373 Fit side-chains outliers start: 20 outliers final: 17 residues processed: 92 average time/residue: 0.1041 time to fit residues: 12.7271 Evaluate side-chains 90 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 30.0000 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: 0.5529 moved from start: 0.9470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3516 Z= 0.320 Angle : 0.831 8.532 4788 Z= 0.446 Chirality : 0.063 0.386 606 Planarity : 0.004 0.022 579 Dihedral : 9.597 55.195 711 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 5.25 % Allowed : 21.00 % Favored : 73.75 % 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: -3.89 (0.35), 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 0.006 0.002 HIS B 239 PHE 0.015 0.003 PHE A 237 TYR 0.020 0.003 TYR C 158 ARG 0.003 0.001 ARG A 180 *********************** 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 106 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.410 Fit side-chains REVERT: A 121 ILE cc_start: 0.4935 (mm) cc_final: 0.4720 (pt) REVERT: A 163 GLU cc_start: 0.6762 (mp0) cc_final: 0.6555 (mp0) REVERT: A 209 TYR cc_start: 0.6260 (OUTLIER) cc_final: 0.5598 (m-10) outliers start: 20 outliers final: 18 residues processed: 98 average time/residue: 0.0921 time to fit residues: 12.3441 Evaluate side-chains 100 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 30.0000 chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN B 222 HIS ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5440 moved from start: 0.9810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3516 Z= 0.241 Angle : 0.742 7.133 4788 Z= 0.396 Chirality : 0.059 0.332 606 Planarity : 0.003 0.022 579 Dihedral : 8.432 49.760 711 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 5.77 % Allowed : 22.31 % Favored : 71.92 % 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: -3.78 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 239 PHE 0.011 0.002 PHE A 237 TYR 0.013 0.002 TYR B 236 ARG 0.002 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.447 Fit side-chains REVERT: A 135 TYR cc_start: 0.5121 (m-10) cc_final: 0.4761 (p90) outliers start: 22 outliers final: 19 residues processed: 94 average time/residue: 0.0910 time to fit residues: 11.6197 Evaluate side-chains 95 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 1.0275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3516 Z= 0.289 Angle : 0.784 7.362 4788 Z= 0.417 Chirality : 0.060 0.374 606 Planarity : 0.003 0.021 579 Dihedral : 8.358 51.716 711 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 5.77 % Allowed : 23.36 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.35), 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 0.006 0.002 HIS B 239 PHE 0.026 0.003 PHE B 171 TYR 0.017 0.002 TYR B 236 ARG 0.003 0.001 ARG A 180 *********************** 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 105 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.412 Fit side-chains REVERT: A 135 TYR cc_start: 0.5180 (m-10) cc_final: 0.4926 (p90) outliers start: 22 outliers final: 17 residues processed: 97 average time/residue: 0.0918 time to fit residues: 12.1436 Evaluate side-chains 96 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 30.0000 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 20.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5362 moved from start: 1.0237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3516 Z= 0.194 Angle : 0.707 9.897 4788 Z= 0.370 Chirality : 0.057 0.292 606 Planarity : 0.002 0.022 579 Dihedral : 6.987 47.569 711 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.20 % Allowed : 24.93 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 239 PHE 0.012 0.002 PHE C 237 TYR 0.020 0.001 TYR A 143 ARG 0.001 0.000 ARG A 180 *********************** 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 105 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.408 Fit side-chains REVERT: A 135 TYR cc_start: 0.5128 (m-10) cc_final: 0.4774 (p90) outliers start: 16 outliers final: 13 residues processed: 96 average time/residue: 0.0967 time to fit residues: 12.6141 Evaluate side-chains 94 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.3980 chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 0.0570 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 overall best weight: 2.0904 ------------------------------------------------------------------------------- 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** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5398 moved from start: 1.0437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3516 Z= 0.215 Angle : 0.757 10.914 4788 Z= 0.386 Chirality : 0.058 0.304 606 Planarity : 0.002 0.022 579 Dihedral : 6.788 45.490 711 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.46 % Allowed : 25.20 % Favored : 70.34 % 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: -3.79 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 239 PHE 0.014 0.002 PHE C 237 TYR 0.018 0.001 TYR A 143 ARG 0.001 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.375 Fit side-chains REVERT: A 135 TYR cc_start: 0.5156 (m-10) cc_final: 0.4819 (p90) outliers start: 17 outliers final: 15 residues processed: 90 average time/residue: 0.0952 time to fit residues: 11.6508 Evaluate side-chains 94 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 30.0000 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5421 moved from start: 1.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3516 Z= 0.235 Angle : 0.800 12.299 4788 Z= 0.408 Chirality : 0.058 0.312 606 Planarity : 0.003 0.021 579 Dihedral : 6.757 45.213 711 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 4.20 % Allowed : 25.72 % Favored : 70.08 % 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 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 239 PHE 0.013 0.002 PHE C 237 TYR 0.018 0.002 TYR A 143 ARG 0.002 0.000 ARG A 180 ********************** 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 99 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.391 Fit side-chains REVERT: A 135 TYR cc_start: 0.5118 (m-10) cc_final: 0.4785 (p90) REVERT: A 192 MET cc_start: 0.6454 (mmt) cc_final: 0.6187 (mmp) REVERT: A 207 MET cc_start: 0.5024 (tmm) cc_final: 0.4758 (tmm) REVERT: A 215 THR cc_start: 0.7088 (p) cc_final: 0.6666 (p) outliers start: 16 outliers final: 16 residues processed: 89 average time/residue: 0.1006 time to fit residues: 12.0001 Evaluate side-chains 97 residues out of total 375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 0.0070 chunk 27 optimal weight: 0.0570 chunk 1 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5439 r_free = 0.5439 target = 0.310605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5662 r_free = 0.5662 target = 0.268447 restraints weight = 23180.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5686 r_free = 0.5686 target = 0.271367 restraints weight = 9319.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5706 r_free = 0.5706 target = 0.273260 restraints weight = 5113.704| |-----------------------------------------------------------------------------| r_work (final): 0.5365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5366 r_free = 0.5366 target_work(ls_wunit_k1) = 0.281 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5357 r_free = 0.5357 target_work(ls_wunit_k1) = 0.281 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5627 moved from start: 1.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3516 Z= 0.203 Angle : 0.756 10.854 4788 Z= 0.385 Chirality : 0.057 0.289 606 Planarity : 0.002 0.021 579 Dihedral : 6.417 43.676 711 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 3.67 % Allowed : 25.98 % Favored : 70.34 % 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: -3.75 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 239 PHE 0.015 0.002 PHE C 237 TYR 0.014 0.001 TYR A 143 ARG 0.001 0.000 ARG C 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1109.63 seconds wall clock time: 20 minutes 51.12 seconds (1251.12 seconds total)