Starting phenix.real_space_refine on Thu Dec 7 23:25:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saq_24953/12_2023/7saq_24953.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saq_24953/12_2023/7saq_24953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saq_24953/12_2023/7saq_24953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saq_24953/12_2023/7saq_24953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saq_24953/12_2023/7saq_24953.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saq_24953/12_2023/7saq_24953.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 35 5.16 5 C 3630 2.51 5 N 885 2.21 5 O 1160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 122": "OD1" <-> "OD2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "C ASP 122": "OD1" <-> "OD2" Residue "D ASP 122": "OD1" <-> "OD2" Residue "E ASP 122": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5710 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "C" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "D" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "E" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "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 Chain: "D" 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: "E" 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: 3.72, per 1000 atoms: 0.65 Number of scatterers: 5710 At special positions: 0 Unit cell: (106.7, 122.1, 45.1, 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 35 16.00 O 1160 8.00 N 885 7.00 C 3630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 253 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 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 145 " " NAG A 302 " - " ASN A 164 " " NAG A 303 " - " ASN A 183 " " NAG A 304 " - " ASN A 151 " " NAG B 301 " - " ASN B 145 " " NAG B 302 " - " ASN B 164 " " NAG B 303 " - " ASN B 183 " " NAG B 304 " - " ASN B 151 " " NAG C 301 " - " ASN C 145 " " NAG C 302 " - " ASN C 164 " " NAG C 303 " - " ASN C 183 " " NAG C 304 " - " ASN C 151 " " NAG D 301 " - " ASN D 145 " " NAG D 302 " - " ASN D 164 " " NAG D 303 " - " ASN D 183 " " NAG D 304 " - " ASN D 151 " " NAG E 301 " - " ASN E 145 " " NAG E 302 " - " ASN E 164 " " NAG E 303 " - " ASN E 183 " " NAG E 304 " - " ASN E 151 " Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 964.1 milliseconds 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 74.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 122 through 126 removed outlier: 6.689A pdb=" N VAL A 123 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE D 126 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR A 125 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 138 removed outlier: 7.067A pdb=" N SER C 130 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA B 131 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR C 132 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N SER D 130 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA C 131 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR D 132 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N SER A 130 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 10.162A pdb=" N VAL D 133 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR A 132 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TYR D 135 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER A 134 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL D 137 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP A 136 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N SER E 130 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA A 131 " --> pdb=" O SER E 130 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N TYR E 132 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 142 through 143 removed outlier: 6.578A pdb=" N ILE A 142 " --> pdb=" O TYR D 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 177 removed outlier: 6.549A pdb=" N ILE B 146 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR C 149 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN B 148 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASN C 151 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU B 150 " --> pdb=" O ASN C 151 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR C 153 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 152 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ASN C 155 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN B 154 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N TYR C 157 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN B 156 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER C 159 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR B 158 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLU C 161 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL B 160 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLU C 163 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N VAL B 162 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N ILE C 165 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN B 164 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N ALA C 167 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR B 166 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL C 169 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLN B 168 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE C 171 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN B 170 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LYS C 173 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER B 172 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL C 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR B 174 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLY C 177 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE B 176 " --> pdb=" O GLY C 177 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE C 146 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR D 149 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN C 148 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASN D 151 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU C 150 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR D 153 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE C 152 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASN D 155 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN C 154 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N TYR D 157 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN C 156 " --> pdb=" O TYR D 157 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER D 159 " --> pdb=" O ASN C 156 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR C 158 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLU D 161 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N VAL C 160 " --> pdb=" O GLU D 161 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU D 163 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N VAL C 162 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N ILE D 165 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN C 164 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N ALA D 167 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR C 166 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL D 169 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN C 168 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE D 171 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN C 170 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LYS D 173 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER C 172 " --> pdb=" O LYS D 173 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL D 175 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR C 174 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLY D 177 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 176 " --> pdb=" O GLY D 177 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL D 162 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU A 163 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASN D 164 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A 165 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR D 166 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A 146 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR E 149 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A 148 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ASN E 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 150 " --> pdb=" O ASN E 151 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N THR E 153 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE A 152 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASN E 155 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN A 154 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N TYR E 157 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN A 156 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N SER E 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYR A 158 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLU E 161 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N VAL A 160 " --> pdb=" O GLU E 161 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLU E 163 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N VAL A 162 " --> pdb=" O GLU E 163 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N ILE E 165 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N ASN A 164 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N ALA E 167 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR A 166 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N VAL E 169 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLN A 168 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N PHE E 171 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN A 170 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LYS E 173 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER A 172 " --> pdb=" O LYS E 173 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL E 175 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR A 174 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY E 177 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 176 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 180 through 187 removed outlier: 6.140A pdb=" N LEU B 181 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE C 184 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ASN B 183 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N ILE C 186 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N THR B 185 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU C 181 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE D 184 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN C 183 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N ILE D 186 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N THR C 185 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE A 184 " --> pdb=" O ASN D 183 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR D 185 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE A 186 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE D 187 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU A 181 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE E 184 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASN A 183 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N ILE E 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N THR A 185 " --> pdb=" O ILE E 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 194 through 198 removed outlier: 6.616A pdb=" N ILE B 195 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR C 198 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR B 197 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE C 195 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR D 198 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR C 197 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 195 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N THR E 198 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR A 197 " --> pdb=" O THR E 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 201 through 205 removed outlier: 6.404A pdb=" N VAL A 202 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLU D 205 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 204 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 230 removed outlier: 6.989A pdb=" N THR C 215 " --> pdb=" O CYS B 214 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 216 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE C 217 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SER B 218 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE C 219 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE B 224 " --> pdb=" O ASN C 223 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL C 225 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU B 226 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET C 227 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N MET B 228 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR D 215 " --> pdb=" O CYS C 214 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU C 216 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE D 217 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SER C 218 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE D 219 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE C 224 " --> pdb=" O ASN D 223 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL D 225 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU C 226 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET D 227 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N MET C 228 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR A 209 " --> pdb=" O MET D 210 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASP D 212 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR A 211 " --> pdb=" O ASP D 212 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N CYS D 214 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N PHE A 213 " --> pdb=" O CYS D 214 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU D 216 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N THR A 215 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N SER D 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N ILE A 217 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N LYS D 220 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE A 219 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N HIS D 222 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL A 221 " --> pdb=" O HIS D 222 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE D 224 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASN A 223 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N LEU D 226 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N VAL A 225 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 10.104A pdb=" N MET D 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N MET A 227 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N VAL D 230 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN A 229 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR E 215 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 216 " --> pdb=" O THR E 215 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE E 217 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER A 218 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE E 219 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE A 224 " --> pdb=" O ASN E 223 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL E 225 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 226 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N MET E 227 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N MET A 228 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 233 through 253 removed outlier: 6.692A pdb=" N THR B 233 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N TYR C 236 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR B 235 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY C 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE B 237 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N SER C 240 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS B 239 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLN C 242 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU B 241 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N SER C 244 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 243 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLU C 246 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN B 245 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N TYR C 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG B 247 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N TYR C 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N GLN B 249 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASP C 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N VAL B 251 " --> pdb=" O ASP C 252 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR C 233 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N TYR D 236 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR C 235 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY D 238 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE C 237 " --> pdb=" O GLY D 238 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N SER D 240 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS C 239 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLN D 242 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU C 241 " --> pdb=" O GLN D 242 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N SER D 244 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 243 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLU D 246 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN C 245 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N TYR D 248 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG C 247 " --> pdb=" O TYR D 248 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N TYR D 250 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N GLN C 249 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ASP D 252 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N VAL C 251 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL D 251 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASP A 252 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N CYS D 253 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A 233 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N TYR E 236 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR A 235 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY E 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 237 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N SER E 240 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N HIS A 239 " --> pdb=" O SER E 240 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N GLN E 242 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU A 241 " --> pdb=" O GLN E 242 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N SER E 244 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 243 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N GLU E 246 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN A 245 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR E 248 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG A 247 " --> pdb=" O TYR E 248 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N TYR E 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N GLN A 249 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASP E 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N VAL A 251 " --> pdb=" O ASP E 252 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 2.33 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: 1749 1.34 - 1.46: 1093 1.46 - 1.58: 2898 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 5800 Sorted by residual: bond pdb=" N VAL E 123 " pdb=" CA VAL E 123 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 9.11e+00 bond pdb=" N VAL D 123 " pdb=" CA VAL D 123 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 9.06e+00 bond pdb=" N VAL A 123 " pdb=" CA VAL A 123 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.19e-02 7.06e+03 8.86e+00 bond pdb=" N VAL C 123 " pdb=" CA VAL C 123 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.19e-02 7.06e+03 8.86e+00 bond pdb=" N VAL B 123 " pdb=" CA VAL B 123 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.19e-02 7.06e+03 8.75e+00 ... (remaining 5795 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.33: 105 106.33 - 112.58: 3194 112.58 - 118.83: 1546 118.83 - 125.08: 3005 125.08 - 131.33: 35 Bond angle restraints: 7885 Sorted by residual: angle pdb=" CA ILE D 121 " pdb=" C ILE D 121 " pdb=" O ILE D 121 " ideal model delta sigma weight residual 121.17 117.47 3.70 1.06e+00 8.90e-01 1.22e+01 angle pdb=" CA ILE E 121 " pdb=" C ILE E 121 " pdb=" O ILE E 121 " ideal model delta sigma weight residual 121.17 117.49 3.68 1.06e+00 8.90e-01 1.20e+01 angle pdb=" CA ILE B 121 " pdb=" C ILE B 121 " pdb=" O ILE B 121 " ideal model delta sigma weight residual 121.17 117.50 3.67 1.06e+00 8.90e-01 1.20e+01 angle pdb=" CA ILE A 121 " pdb=" C ILE A 121 " pdb=" O ILE A 121 " ideal model delta sigma weight residual 121.17 117.51 3.66 1.06e+00 8.90e-01 1.19e+01 angle pdb=" CA ILE C 121 " pdb=" C ILE C 121 " pdb=" O ILE C 121 " ideal model delta sigma weight residual 121.17 117.55 3.62 1.06e+00 8.90e-01 1.17e+01 ... (remaining 7880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 3391 17.07 - 34.14: 257 34.14 - 51.21: 57 51.21 - 68.28: 30 68.28 - 85.36: 10 Dihedral angle restraints: 3745 sinusoidal: 1715 harmonic: 2030 Sorted by residual: dihedral pdb=" CA GLU B 246 " pdb=" C GLU B 246 " pdb=" N ARG B 247 " pdb=" CA ARG B 247 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA GLU C 246 " pdb=" C GLU C 246 " pdb=" N ARG C 247 " pdb=" CA ARG C 247 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA GLU E 246 " pdb=" C GLU E 246 " pdb=" N ARG E 247 " pdb=" CA ARG E 247 " ideal model delta harmonic sigma weight residual 180.00 161.57 18.43 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 3742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 720 0.060 - 0.121: 243 0.121 - 0.181: 27 0.181 - 0.241: 0 0.241 - 0.301: 15 Chirality restraints: 1005 Sorted by residual: chirality pdb=" C1 NAG C 302 " pdb=" ND2 ASN C 164 " pdb=" C2 NAG C 302 " pdb=" O5 NAG C 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1 NAG D 302 " pdb=" ND2 ASN D 164 " pdb=" C2 NAG D 302 " pdb=" O5 NAG D 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1 NAG E 302 " pdb=" ND2 ASN E 164 " pdb=" C2 NAG E 302 " pdb=" O5 NAG E 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 1002 not shown) Planarity restraints: 970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 302 " 0.324 2.00e-02 2.50e+03 2.81e-01 9.90e+02 pdb=" C7 NAG B 302 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG B 302 " 0.055 2.00e-02 2.50e+03 pdb=" N2 NAG B 302 " -0.498 2.00e-02 2.50e+03 pdb=" O7 NAG B 302 " 0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 302 " 0.324 2.00e-02 2.50e+03 2.81e-01 9.90e+02 pdb=" C7 NAG D 302 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG D 302 " 0.055 2.00e-02 2.50e+03 pdb=" N2 NAG D 302 " -0.498 2.00e-02 2.50e+03 pdb=" O7 NAG D 302 " 0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 302 " 0.324 2.00e-02 2.50e+03 2.81e-01 9.90e+02 pdb=" C7 NAG A 302 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG A 302 " 0.055 2.00e-02 2.50e+03 pdb=" N2 NAG A 302 " -0.498 2.00e-02 2.50e+03 pdb=" O7 NAG A 302 " 0.187 2.00e-02 2.50e+03 ... (remaining 967 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 548 2.77 - 3.30: 5087 3.30 - 3.84: 9748 3.84 - 4.37: 10559 4.37 - 4.90: 17198 Nonbonded interactions: 43140 Sorted by model distance: nonbonded pdb=" OG1 THR E 231 " pdb=" OG1 THR E 234 " model vdw 2.241 2.440 nonbonded pdb=" OG1 THR A 231 " pdb=" OG1 THR A 234 " model vdw 2.241 2.440 nonbonded pdb=" OG1 THR D 231 " pdb=" OG1 THR D 234 " model vdw 2.241 2.440 nonbonded pdb=" OG1 THR B 231 " pdb=" OG1 THR B 234 " model vdw 2.241 2.440 nonbonded pdb=" OG1 THR C 231 " pdb=" OG1 THR C 234 " model vdw 2.241 2.440 ... (remaining 43135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 19.680 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5800 Z= 0.368 Angle : 0.839 5.358 7885 Z= 0.493 Chirality : 0.065 0.301 1005 Planarity : 0.022 0.281 950 Dihedral : 14.709 85.356 2430 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % 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: -3.19 (0.27), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 239 PHE 0.010 0.002 PHE E 213 TYR 0.104 0.005 TYR A 125 ARG 0.001 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.696 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 1.4114 time to fit residues: 91.3298 Evaluate side-chains 53 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.626 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 249 GLN B 154 ASN B 249 GLN C 154 ASN C 156 ASN C 249 GLN D 154 ASN D 249 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5800 Z= 0.322 Angle : 0.749 6.736 7885 Z= 0.416 Chirality : 0.063 0.482 1005 Planarity : 0.003 0.024 950 Dihedral : 8.242 43.486 1165 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.90 % Allowed : 10.79 % Favored : 87.30 % 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: -2.55 (0.30), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 239 PHE 0.008 0.001 PHE B 213 TYR 0.028 0.003 TYR D 125 ARG 0.001 0.000 ARG E 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 72 average time/residue: 1.4074 time to fit residues: 105.6113 Evaluate side-chains 67 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.577 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0772 time to fit residues: 1.0861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 58 optimal weight: 40.0000 chunk 20 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5800 Z= 0.415 Angle : 0.797 4.909 7885 Z= 0.444 Chirality : 0.068 0.571 1005 Planarity : 0.003 0.020 950 Dihedral : 7.523 34.203 1165 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.33 % Allowed : 15.40 % Favored : 81.27 % 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: -2.73 (0.28), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.004 HIS C 239 PHE 0.010 0.002 PHE B 213 TYR 0.021 0.003 TYR E 135 ARG 0.001 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 0.664 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 82 average time/residue: 1.2255 time to fit residues: 105.2111 Evaluate side-chains 74 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.627 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 0.6544 time to fit residues: 5.1140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN C 168 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 5800 Z= 0.401 Angle : 0.785 5.628 7885 Z= 0.433 Chirality : 0.069 0.625 1005 Planarity : 0.003 0.020 950 Dihedral : 7.380 34.258 1165 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.29 % Allowed : 17.78 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.27), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.003 HIS E 239 PHE 0.013 0.002 PHE C 213 TYR 0.021 0.003 TYR E 135 ARG 0.001 0.000 ARG E 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 65 time to evaluate : 0.594 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 81 average time/residue: 1.3054 time to fit residues: 110.4926 Evaluate side-chains 78 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 10 residues processed: 7 average time/residue: 0.6192 time to fit residues: 5.5613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5800 Z= 0.262 Angle : 0.683 5.072 7885 Z= 0.376 Chirality : 0.064 0.629 1005 Planarity : 0.003 0.019 950 Dihedral : 6.766 31.431 1165 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.65 % Allowed : 19.37 % Favored : 76.98 % 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: -3.03 (0.27), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 239 PHE 0.009 0.002 PHE C 213 TYR 0.017 0.002 TYR E 248 ARG 0.001 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 67 time to evaluate : 0.647 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 81 average time/residue: 1.3771 time to fit residues: 116.2843 Evaluate side-chains 79 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.3551 time to fit residues: 3.2875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 15 optimal weight: 0.0370 chunk 62 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 overall best weight: 5.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5800 Z= 0.329 Angle : 0.732 5.402 7885 Z= 0.403 Chirality : 0.066 0.628 1005 Planarity : 0.003 0.020 950 Dihedral : 6.876 32.153 1165 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.33 % Allowed : 20.32 % Favored : 76.35 % 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: -3.14 (0.27), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS E 239 PHE 0.009 0.002 PHE C 213 TYR 0.021 0.003 TYR E 248 ARG 0.001 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 64 time to evaluate : 0.626 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 79 average time/residue: 1.3592 time to fit residues: 112.1653 Evaluate side-chains 74 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 5 average time/residue: 0.2813 time to fit residues: 2.5156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 GLN C 168 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 5800 Z= 0.443 Angle : 0.819 7.986 7885 Z= 0.447 Chirality : 0.072 0.796 1005 Planarity : 0.003 0.021 950 Dihedral : 7.519 34.018 1165 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.33 % Allowed : 20.63 % Favored : 76.03 % 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: -3.29 (0.26), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS E 239 PHE 0.011 0.002 PHE C 213 TYR 0.023 0.003 TYR E 248 ARG 0.001 0.000 ARG E 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 0.658 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 84 average time/residue: 1.2776 time to fit residues: 112.0488 Evaluate side-chains 81 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 0.644 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.6212 time to fit residues: 4.8896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN B 138 GLN C 168 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5800 Z= 0.346 Angle : 0.760 7.236 7885 Z= 0.417 Chirality : 0.068 0.687 1005 Planarity : 0.003 0.021 950 Dihedral : 7.181 35.550 1165 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.70 % Allowed : 21.11 % Favored : 76.19 % 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: -3.32 (0.26), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS B 239 PHE 0.010 0.002 PHE A 213 TYR 0.022 0.003 TYR E 248 ARG 0.001 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.646 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 14 residues processed: 80 average time/residue: 1.3830 time to fit residues: 115.2273 Evaluate side-chains 77 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.635 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.0826 time to fit residues: 1.3935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5800 Z= 0.336 Angle : 0.761 6.623 7885 Z= 0.416 Chirality : 0.069 0.652 1005 Planarity : 0.003 0.023 950 Dihedral : 7.048 33.884 1165 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.54 % Allowed : 21.75 % Favored : 75.71 % 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: -3.31 (0.27), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 239 PHE 0.010 0.002 PHE A 213 TYR 0.022 0.003 TYR E 248 ARG 0.001 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.659 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 81 average time/residue: 1.2913 time to fit residues: 109.1289 Evaluate side-chains 77 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.0690 time to fit residues: 1.2059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN C 168 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5800 Z= 0.297 Angle : 0.734 7.523 7885 Z= 0.400 Chirality : 0.067 0.626 1005 Planarity : 0.003 0.022 950 Dihedral : 6.801 34.229 1165 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.54 % Allowed : 22.06 % 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: -3.27 (0.27), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 239 PHE 0.009 0.002 PHE A 213 TYR 0.021 0.002 TYR E 248 ARG 0.001 0.000 ARG B 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.648 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 80 average time/residue: 1.2818 time to fit residues: 107.0560 Evaluate side-chains 78 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.4554 time to fit residues: 2.8054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN C 168 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.148947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.121596 restraints weight = 6077.085| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 2.49 r_work: 0.4222 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4100 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5800 Z= 0.266 Angle : 0.716 7.652 7885 Z= 0.390 Chirality : 0.066 0.601 1005 Planarity : 0.003 0.024 950 Dihedral : 6.718 33.795 1165 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.06 % Allowed : 22.70 % Favored : 75.24 % 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: -3.21 (0.27), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 239 PHE 0.009 0.002 PHE D 171 TYR 0.020 0.002 TYR E 248 ARG 0.001 0.000 ARG B 180 =============================================================================== Job complete usr+sys time: 2222.03 seconds wall clock time: 40 minutes 26.56 seconds (2426.56 seconds total)