Starting phenix.real_space_refine on Wed Mar 4 03:09:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6i_28884/03_2026/8f6i_28884.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6i_28884/03_2026/8f6i_28884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f6i_28884/03_2026/8f6i_28884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6i_28884/03_2026/8f6i_28884.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6i_28884/03_2026/8f6i_28884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6i_28884/03_2026/8f6i_28884.cif" } resolution = 4.03 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.013 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: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 28 5.16 5 C 6620 2.51 5 N 1734 2.21 5 O 1979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10367 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2132 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 6, 'TRANS': 269} Chain breaks: 1 Chain: "A" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2112 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 5, 'TRANS': 268} Chain breaks: 1 Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1474 Classifications: {'peptide': 192} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "F" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1589 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "C" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1474 Classifications: {'peptide': 192} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "D" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1580 Classifications: {'peptide': 208} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 195} Chain breaks: 2 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.25, per 1000 atoms: 0.22 Number of scatterers: 10367 At special positions: 0 Unit cell: (67.977, 157.534, 149.981, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 28 16.00 O 1979 8.00 N 1734 7.00 C 6620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 213 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 587.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS B 263 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 285 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 250 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 234 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 155 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 285 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS A 263 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" ND1 HIS B 250 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 234 " pdb=" ZN B 303 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS B 155 " 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 22 sheets defined 31.9% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 8 through 37 removed outlier: 3.596A pdb=" N LYS B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 25 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 28 " --> pdb=" O THR B 24 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 61 removed outlier: 3.821A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 60 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 103 removed outlier: 3.721A pdb=" N LEU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 115 through 141 removed outlier: 4.030A pdb=" N VAL B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 175 removed outlier: 4.194A pdb=" N LEU B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N HIS B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 170 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR B 175 " --> pdb=" O VAL B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 208 removed outlier: 3.795A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 226 Processing helix chain 'B' and resid 258 through 277 removed outlier: 3.673A pdb=" N SER B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 34 removed outlier: 3.677A pdb=" N THR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 64 removed outlier: 3.531A pdb=" N LEU A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 105 removed outlier: 3.769A pdb=" N GLU A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 140 removed outlier: 4.130A pdb=" N GLY A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 176 removed outlier: 4.229A pdb=" N LEU A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 208 removed outlier: 3.632A pdb=" N LEU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 258 through 277 Processing helix chain 'E' and resid 123 through 129 Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.939A pdb=" N GLU E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 185 through 189' Processing helix chain 'F' and resid 31 through 35 removed outlier: 3.799A pdb=" N SER F 34 " --> pdb=" O THR F 31 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER F 35 " --> pdb=" O ILE F 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 31 through 35' Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.702A pdb=" N LEU C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 128' Processing helix chain 'C' and resid 185 through 189 removed outlier: 3.741A pdb=" N GLU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 185 through 189' Processing helix chain 'D' and resid 65 through 68 removed outlier: 3.710A pdb=" N LYS D 68 " --> pdb=" O ASP D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 171 through 175 Processing sheet with id=AA1, first strand: chain 'B' and resid 232 through 241 removed outlier: 6.349A pdb=" N LEU B 233 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP B 235 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS B 250 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL B 245 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE B 283 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE B 247 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N HIS B 285 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE B 249 " --> pdb=" O HIS B 285 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP B 287 " --> pdb=" O PHE B 249 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU B 251 " --> pdb=" O ASP B 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 241 removed outlier: 5.920A pdb=" N LEU A 233 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLU A 252 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP A 235 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N HIS A 250 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 283 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 249 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS A 285 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 6 through 8 removed outlier: 3.701A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 11 through 14 Processing sheet with id=AA5, first strand: chain 'E' and resid 46 through 50 removed outlier: 6.835A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR E 86 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 116 through 120 removed outlier: 3.854A pdb=" N VAL E 135 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E 134 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR E 175 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER E 178 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 147 through 148 Processing sheet with id=AA8, first strand: chain 'F' and resid 8 through 10 Processing sheet with id=AA9, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.866A pdb=" N THR F 128 " --> pdb=" O GLY F 13 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 127 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.866A pdb=" N THR F 128 " --> pdb=" O GLY F 13 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 127 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N CYS F 99 " --> pdb=" O TRP F 121 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TRP F 121 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG F 101 " --> pdb=" O ASP F 119 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP F 119 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.550A pdb=" N SER F 137 " --> pdb=" O LYS F 160 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU F 141 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.550A pdb=" N SER F 137 " --> pdb=" O LYS F 160 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU F 141 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 192 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 167 through 171 removed outlier: 4.118A pdb=" N THR F 168 " --> pdb=" O ASN F 216 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN F 216 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER F 170 " --> pdb=" O ASN F 214 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN F 214 " --> pdb=" O SER F 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AB6, first strand: chain 'C' and resid 11 through 14 removed outlier: 3.571A pdb=" N THR C 86 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TYR C 50 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 38 " --> pdb=" O LYS C 46 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR C 50 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 11 through 14 removed outlier: 6.021A pdb=" N ILE C 92 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N THR C 99 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER C 94 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.795A pdb=" N VAL C 135 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA C 132 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N TYR C 175 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 8 through 10 removed outlier: 3.621A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 24 " --> pdb=" O SER D 10 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 84 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR D 81 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 62 through 63 removed outlier: 6.700A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N CYS D 99 " --> pdb=" O TRP D 121 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TRP D 121 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG D 101 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 62 through 63 removed outlier: 6.700A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 137 through 141 removed outlier: 4.080A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 167 through 169 removed outlier: 3.677A pdb=" N CYS D 213 " --> pdb=" O LYS D 226 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS D 226 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D 215 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 224 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS D 217 " --> pdb=" O THR D 222 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1359 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: 1.76 Time building geometry restraints manager: 1.05 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: 3303 1.34 - 1.46: 2572 1.46 - 1.58: 4672 1.58 - 1.70: 0 1.70 - 1.81: 38 Bond restraints: 10585 Sorted by residual: bond pdb=" CB GLU F 92 " pdb=" CG GLU F 92 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.06e-01 bond pdb=" CA ASP C 2 " pdb=" CB ASP C 2 " ideal model delta sigma weight residual 1.527 1.550 -0.023 2.48e-02 1.63e+03 8.64e-01 bond pdb=" CG PRO C 9 " pdb=" CD PRO C 9 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.32e-01 bond pdb=" C GLN C 39 " pdb=" N LYS C 40 " ideal model delta sigma weight residual 1.339 1.299 0.040 5.57e-02 3.22e+02 5.24e-01 bond pdb=" CG GLU F 92 " pdb=" CD GLU F 92 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.21e-01 ... (remaining 10580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 13925 1.21 - 2.42: 360 2.42 - 3.62: 93 3.62 - 4.83: 20 4.83 - 6.04: 7 Bond angle restraints: 14405 Sorted by residual: angle pdb=" C LEU A 34 " pdb=" N TYR A 35 " pdb=" CA TYR A 35 " ideal model delta sigma weight residual 121.54 126.31 -4.77 1.91e+00 2.74e-01 6.23e+00 angle pdb=" N ARG D 111 " pdb=" CA ARG D 111 " pdb=" C ARG D 111 " ideal model delta sigma weight residual 110.80 115.45 -4.65 2.13e+00 2.20e-01 4.77e+00 angle pdb=" N ASP F 93 " pdb=" CA ASP F 93 " pdb=" C ASP F 93 " ideal model delta sigma weight residual 114.09 110.71 3.38 1.55e+00 4.16e-01 4.77e+00 angle pdb=" N ASP B 181 " pdb=" CA ASP B 181 " pdb=" CB ASP B 181 " ideal model delta sigma weight residual 113.65 110.65 3.00 1.47e+00 4.63e-01 4.16e+00 angle pdb=" N HIS D 112 " pdb=" CA HIS D 112 " pdb=" C HIS D 112 " ideal model delta sigma weight residual 107.75 111.53 -3.78 1.86e+00 2.89e-01 4.12e+00 ... (remaining 14400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5670 17.75 - 35.51: 506 35.51 - 53.26: 85 53.26 - 71.01: 12 71.01 - 88.77: 9 Dihedral angle restraints: 6282 sinusoidal: 2355 harmonic: 3927 Sorted by residual: dihedral pdb=" CB CYS D 157 " pdb=" SG CYS D 157 " pdb=" SG CYS D 213 " pdb=" CB CYS D 213 " ideal model delta sinusoidal sigma weight residual -86.00 -174.77 88.77 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS C 24 " pdb=" SG CYS C 24 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual 93.00 169.27 -76.27 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS D 25 " pdb=" SG CYS D 25 " pdb=" SG CYS D 99 " pdb=" CB CYS D 99 " ideal model delta sinusoidal sigma weight residual 93.00 161.97 -68.97 1 1.00e+01 1.00e-02 6.16e+01 ... (remaining 6279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 977 0.026 - 0.052: 443 0.052 - 0.077: 127 0.077 - 0.103: 96 0.103 - 0.129: 35 Chirality restraints: 1678 Sorted by residual: chirality pdb=" CA ILE C 49 " pdb=" N ILE C 49 " pdb=" C ILE C 49 " pdb=" CB ILE C 49 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA VAL C 59 " pdb=" N VAL C 59 " pdb=" C VAL C 59 " pdb=" CB VAL C 59 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE E 98 " pdb=" N ILE E 98 " pdb=" C ILE E 98 " pdb=" CB ILE E 98 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1675 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 95 " -0.009 2.00e-02 2.50e+03 1.14e-02 3.25e+00 pdb=" CG TRP E 95 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP E 95 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP E 95 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP E 95 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP E 95 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 95 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 95 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 95 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 95 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 165 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO F 166 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 166 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 166 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 59 " 0.027 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO E 60 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " 0.023 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 124 2.64 - 3.20: 9490 3.20 - 3.77: 15411 3.77 - 4.33: 20115 4.33 - 4.90: 32598 Nonbonded interactions: 77738 Sorted by model distance: nonbonded pdb=" OD2 ASP B 287 " pdb="ZN ZN B 302 " model vdw 2.070 2.230 nonbonded pdb=" OD1 ASP A 287 " pdb="ZN ZN A 301 " model vdw 2.071 2.230 nonbonded pdb=" OD1 ASP B 47 " pdb="ZN ZN B 303 " model vdw 2.092 2.230 nonbonded pdb=" OD1 ASP B 287 " pdb="ZN ZN B 301 " model vdw 2.093 2.230 nonbonded pdb=" OD2 ASP B 51 " pdb="ZN ZN B 303 " model vdw 2.100 2.230 ... (remaining 77733 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 63 or resid 78 through 303)) selection = (chain 'B' and (resid 9 through 63 or resid 78 through 292 or resid 301 through \ 303)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = (chain 'F' and resid 5 through 230) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.690 Find NCS groups from input model: 0.400 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: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.002 0.040 10602 Z= 0.097 Angle : 0.504 6.040 14419 Z= 0.254 Chirality : 0.039 0.129 1678 Planarity : 0.003 0.042 1808 Dihedral : 13.671 86.096 3729 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.99 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.24), residues: 1323 helix: 1.17 (0.27), residues: 377 sheet: 0.45 (0.27), residues: 379 loop : -0.78 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 111 TYR 0.014 0.001 TYR F 193 PHE 0.018 0.001 PHE A 91 TRP 0.029 0.001 TRP E 95 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00216 (10585) covalent geometry : angle 0.50426 (14405) SS BOND : bond 0.00159 ( 7) SS BOND : angle 0.52833 ( 14) hydrogen bonds : bond 0.29427 ( 464) hydrogen bonds : angle 9.20416 ( 1359) metal coordination : bond 0.00287 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8386 (pp30) cc_final: 0.7898 (pp30) REVERT: E 145 GLU cc_start: 0.8161 (mp0) cc_final: 0.7944 (mp0) REVERT: F 161 ASP cc_start: 0.7369 (m-30) cc_final: 0.7169 (m-30) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0892 time to fit residues: 20.2015 Evaluate side-chains 118 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.0570 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.126804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.097992 restraints weight = 25290.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.096449 restraints weight = 32480.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097389 restraints weight = 24641.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.098395 restraints weight = 15042.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.100488 restraints weight = 12714.897| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10602 Z= 0.183 Angle : 0.585 7.846 14419 Z= 0.314 Chirality : 0.042 0.162 1678 Planarity : 0.004 0.046 1808 Dihedral : 4.009 24.399 1446 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.37 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.23), residues: 1323 helix: 1.56 (0.26), residues: 388 sheet: 0.46 (0.27), residues: 360 loop : -0.86 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 202 TYR 0.016 0.001 TYR F 193 PHE 0.020 0.001 PHE A 249 TRP 0.026 0.001 TRP E 95 HIS 0.007 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00394 (10585) covalent geometry : angle 0.58528 (14405) SS BOND : bond 0.00271 ( 7) SS BOND : angle 0.70333 ( 14) hydrogen bonds : bond 0.06152 ( 464) hydrogen bonds : angle 5.98308 ( 1359) metal coordination : bond 0.00240 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.373 Fit side-chains REVERT: B 98 LEU cc_start: 0.9627 (tp) cc_final: 0.9413 (tp) REVERT: A 33 TRP cc_start: 0.7139 (t-100) cc_final: 0.6587 (t-100) REVERT: A 88 GLN cc_start: 0.8576 (pp30) cc_final: 0.8127 (pp30) REVERT: A 191 TYR cc_start: 0.7880 (t80) cc_final: 0.7679 (t80) REVERT: A 274 LYS cc_start: 0.9192 (ttmt) cc_final: 0.8974 (ttmm) REVERT: E 91 GLN cc_start: 0.8956 (pp30) cc_final: 0.8496 (pp30) REVERT: E 140 ASN cc_start: 0.8461 (m-40) cc_final: 0.8212 (m-40) REVERT: C 95 TRP cc_start: 0.7755 (t60) cc_final: 0.6695 (t60) REVERT: D 80 ASN cc_start: 0.6177 (m-40) cc_final: 0.5926 (m-40) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0896 time to fit residues: 21.6956 Evaluate side-chains 124 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN A 163 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.126829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.097726 restraints weight = 25340.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096670 restraints weight = 31706.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097792 restraints weight = 24474.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097948 restraints weight = 16370.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100586 restraints weight = 13397.883| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10602 Z= 0.160 Angle : 0.566 7.329 14419 Z= 0.295 Chirality : 0.041 0.168 1678 Planarity : 0.004 0.064 1808 Dihedral : 4.056 22.544 1446 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.29 % Favored : 94.56 % Rotamer: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.23), residues: 1323 helix: 1.52 (0.26), residues: 392 sheet: 0.31 (0.27), residues: 362 loop : -0.93 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 62 TYR 0.012 0.001 TYR E 50 PHE 0.016 0.001 PHE A 249 TRP 0.033 0.002 TRP E 95 HIS 0.006 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00355 (10585) covalent geometry : angle 0.56547 (14405) SS BOND : bond 0.00256 ( 7) SS BOND : angle 0.86058 ( 14) hydrogen bonds : bond 0.05254 ( 464) hydrogen bonds : angle 5.54703 ( 1359) metal coordination : bond 0.00147 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.402 Fit side-chains REVERT: A 88 GLN cc_start: 0.8566 (pp30) cc_final: 0.8140 (pp30) REVERT: A 168 LEU cc_start: 0.9093 (pp) cc_final: 0.8870 (mt) REVERT: A 191 TYR cc_start: 0.7851 (t80) cc_final: 0.7630 (t80) REVERT: E 5 MET cc_start: 0.8958 (mmt) cc_final: 0.8637 (mmm) REVERT: E 91 GLN cc_start: 0.8864 (pp30) cc_final: 0.8432 (pp30) REVERT: E 95 TRP cc_start: 0.8329 (OUTLIER) cc_final: 0.8092 (t60) REVERT: E 140 ASN cc_start: 0.8541 (m-40) cc_final: 0.8277 (m-40) REVERT: F 223 LYS cc_start: 0.8506 (tppt) cc_final: 0.8098 (mmtt) REVERT: D 131 ASN cc_start: 0.6973 (m-40) cc_final: 0.6761 (m110) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.0802 time to fit residues: 19.3891 Evaluate side-chains 124 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 105 optimal weight: 0.0370 chunk 130 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.127586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.098417 restraints weight = 25229.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.099497 restraints weight = 35657.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100112 restraints weight = 21025.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.101170 restraints weight = 13774.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.101574 restraints weight = 12046.981| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10602 Z= 0.136 Angle : 0.553 7.069 14419 Z= 0.286 Chirality : 0.041 0.147 1678 Planarity : 0.004 0.063 1808 Dihedral : 4.040 22.671 1446 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.23), residues: 1323 helix: 1.47 (0.26), residues: 389 sheet: 0.34 (0.27), residues: 362 loop : -0.90 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 62 TYR 0.012 0.001 TYR E 50 PHE 0.013 0.001 PHE A 249 TRP 0.019 0.001 TRP A 178 HIS 0.008 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00300 (10585) covalent geometry : angle 0.55215 (14405) SS BOND : bond 0.00508 ( 7) SS BOND : angle 1.13379 ( 14) hydrogen bonds : bond 0.04567 ( 464) hydrogen bonds : angle 5.21995 ( 1359) metal coordination : bond 0.00306 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8545 (pp30) cc_final: 0.8060 (pp30) REVERT: E 91 GLN cc_start: 0.8874 (pp30) cc_final: 0.8133 (pp30) REVERT: E 119 ILE cc_start: 0.7389 (mp) cc_final: 0.6913 (pt) REVERT: E 140 ASN cc_start: 0.8504 (m-40) cc_final: 0.8231 (m-40) REVERT: F 50 TRP cc_start: 0.8779 (t60) cc_final: 0.8350 (t60) REVERT: F 160 LYS cc_start: 0.8703 (tppt) cc_final: 0.7971 (tppt) REVERT: F 187 LEU cc_start: 0.8572 (tp) cc_final: 0.7938 (pp) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.0843 time to fit residues: 20.1881 Evaluate side-chains 122 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 10.0000 chunk 113 optimal weight: 0.4980 chunk 22 optimal weight: 0.1980 chunk 59 optimal weight: 0.0770 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 38 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.129363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.101285 restraints weight = 25164.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.100532 restraints weight = 32690.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.101756 restraints weight = 24500.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102041 restraints weight = 15244.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.104831 restraints weight = 12876.698| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10602 Z= 0.107 Angle : 0.546 6.326 14419 Z= 0.278 Chirality : 0.041 0.154 1678 Planarity : 0.004 0.065 1808 Dihedral : 3.938 22.559 1446 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.39 % Rotamer: Outliers : 0.09 % Allowed : 2.82 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.23), residues: 1323 helix: 1.51 (0.26), residues: 386 sheet: 0.20 (0.26), residues: 379 loop : -0.78 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 239 TYR 0.011 0.001 TYR B 175 PHE 0.018 0.001 PHE A 49 TRP 0.028 0.001 TRP E 95 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00229 (10585) covalent geometry : angle 0.54582 (14405) SS BOND : bond 0.00336 ( 7) SS BOND : angle 0.80230 ( 14) hydrogen bonds : bond 0.04018 ( 464) hydrogen bonds : angle 4.93579 ( 1359) metal coordination : bond 0.00082 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 119 ILE cc_start: 0.7265 (mp) cc_final: 0.6908 (pt) REVERT: F 160 LYS cc_start: 0.8705 (tppt) cc_final: 0.7937 (tppt) REVERT: F 187 LEU cc_start: 0.8489 (tp) cc_final: 0.7992 (pp) REVERT: C 48 LEU cc_start: 0.9193 (mt) cc_final: 0.8846 (mp) REVERT: C 95 TRP cc_start: 0.7889 (t60) cc_final: 0.6951 (t60) REVERT: D 50 TRP cc_start: 0.8435 (t60) cc_final: 0.8226 (t60) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.0899 time to fit residues: 23.0044 Evaluate side-chains 133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.128039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.099957 restraints weight = 25321.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097723 restraints weight = 31467.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.099079 restraints weight = 22611.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.099796 restraints weight = 13925.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.101269 restraints weight = 12373.267| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10602 Z= 0.131 Angle : 0.570 8.888 14419 Z= 0.289 Chirality : 0.041 0.143 1678 Planarity : 0.004 0.067 1808 Dihedral : 3.967 22.475 1446 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.23), residues: 1323 helix: 1.45 (0.26), residues: 391 sheet: 0.25 (0.27), residues: 378 loop : -0.81 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 62 TYR 0.021 0.001 TYR F 193 PHE 0.013 0.001 PHE A 249 TRP 0.049 0.001 TRP E 95 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00295 (10585) covalent geometry : angle 0.56968 (14405) SS BOND : bond 0.00602 ( 7) SS BOND : angle 1.05931 ( 14) hydrogen bonds : bond 0.03871 ( 464) hydrogen bonds : angle 4.86207 ( 1359) metal coordination : bond 0.00152 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.351 Fit side-chains REVERT: A 88 GLN cc_start: 0.8532 (pp30) cc_final: 0.8270 (pp30) REVERT: A 102 TYR cc_start: 0.8326 (t80) cc_final: 0.8034 (t80) REVERT: E 119 ILE cc_start: 0.7278 (mp) cc_final: 0.7046 (pt) REVERT: E 140 ASN cc_start: 0.8420 (m-40) cc_final: 0.8212 (m-40) REVERT: F 50 TRP cc_start: 0.8788 (t60) cc_final: 0.8358 (t60) REVERT: F 160 LYS cc_start: 0.8672 (tppt) cc_final: 0.7928 (tppt) REVERT: F 187 LEU cc_start: 0.8816 (tp) cc_final: 0.8237 (pp) REVERT: F 223 LYS cc_start: 0.8234 (mmpt) cc_final: 0.7644 (mmpt) REVERT: D 131 ASN cc_start: 0.6539 (m110) cc_final: 0.6314 (m110) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0841 time to fit residues: 21.1900 Evaluate side-chains 128 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 111 optimal weight: 0.0010 chunk 86 optimal weight: 0.3980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.128897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.099981 restraints weight = 25281.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099326 restraints weight = 31637.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100346 restraints weight = 22779.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.101176 restraints weight = 14389.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102565 restraints weight = 12525.740| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 10602 Z= 0.130 Angle : 0.570 6.721 14419 Z= 0.292 Chirality : 0.041 0.211 1678 Planarity : 0.005 0.077 1808 Dihedral : 4.029 22.021 1446 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.23), residues: 1323 helix: 1.54 (0.27), residues: 388 sheet: 0.31 (0.27), residues: 377 loop : -0.82 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 67 TYR 0.026 0.001 TYR A 156 PHE 0.018 0.001 PHE B 59 TRP 0.045 0.001 TRP E 95 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00301 (10585) covalent geometry : angle 0.56985 (14405) SS BOND : bond 0.00324 ( 7) SS BOND : angle 0.66905 ( 14) hydrogen bonds : bond 0.03676 ( 464) hydrogen bonds : angle 4.78829 ( 1359) metal coordination : bond 0.00112 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.316 Fit side-chains REVERT: A 88 GLN cc_start: 0.8489 (pp30) cc_final: 0.8178 (pp30) REVERT: A 102 TYR cc_start: 0.8257 (t80) cc_final: 0.7999 (t80) REVERT: F 160 LYS cc_start: 0.8705 (tppt) cc_final: 0.7936 (tppt) REVERT: F 187 LEU cc_start: 0.8423 (tp) cc_final: 0.7880 (pp) REVERT: C 95 TRP cc_start: 0.8024 (t60) cc_final: 0.7046 (t60) REVERT: D 111 ARG cc_start: 0.6579 (ptm-80) cc_final: 0.5912 (ttp80) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0900 time to fit residues: 22.4264 Evaluate side-chains 131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 13 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 46 optimal weight: 0.0770 chunk 74 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 127 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.128275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.099821 restraints weight = 25122.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097532 restraints weight = 31098.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.098855 restraints weight = 25037.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100113 restraints weight = 15032.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100645 restraints weight = 12894.657| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10602 Z= 0.135 Angle : 0.575 7.114 14419 Z= 0.293 Chirality : 0.042 0.181 1678 Planarity : 0.004 0.080 1808 Dihedral : 4.070 22.097 1446 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.24), residues: 1323 helix: 1.56 (0.27), residues: 385 sheet: 0.28 (0.27), residues: 379 loop : -0.74 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 67 TYR 0.012 0.001 TYR E 50 PHE 0.012 0.001 PHE E 141 TRP 0.057 0.002 TRP E 95 HIS 0.006 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00312 (10585) covalent geometry : angle 0.57436 (14405) SS BOND : bond 0.00359 ( 7) SS BOND : angle 0.95438 ( 14) hydrogen bonds : bond 0.03661 ( 464) hydrogen bonds : angle 4.77922 ( 1359) metal coordination : bond 0.00208 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.7916 (ptmm) cc_final: 0.7573 (ptmm) REVERT: B 201 TYR cc_start: 0.8297 (t80) cc_final: 0.7989 (t80) REVERT: A 98 LEU cc_start: 0.9242 (mp) cc_final: 0.8989 (mp) REVERT: A 102 TYR cc_start: 0.8309 (t80) cc_final: 0.8048 (t80) REVERT: A 109 ASN cc_start: 0.7696 (p0) cc_final: 0.7317 (t0) REVERT: F 160 LYS cc_start: 0.8709 (tppt) cc_final: 0.7989 (tppt) REVERT: F 187 LEU cc_start: 0.8609 (tp) cc_final: 0.8042 (pp) REVERT: D 111 ARG cc_start: 0.6831 (ptm-80) cc_final: 0.6116 (ttp80) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0834 time to fit residues: 19.9428 Evaluate side-chains 129 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.127383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.099373 restraints weight = 24978.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.097344 restraints weight = 35170.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098515 restraints weight = 26830.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.100586 restraints weight = 15783.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.100816 restraints weight = 11868.496| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10602 Z= 0.150 Angle : 0.589 6.693 14419 Z= 0.303 Chirality : 0.042 0.174 1678 Planarity : 0.005 0.075 1808 Dihedral : 4.127 21.984 1446 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.23), residues: 1323 helix: 1.52 (0.27), residues: 385 sheet: 0.46 (0.27), residues: 367 loop : -0.84 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 67 TYR 0.014 0.001 TYR A 191 PHE 0.020 0.001 PHE A 277 TRP 0.042 0.002 TRP E 95 HIS 0.005 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00350 (10585) covalent geometry : angle 0.58814 (14405) SS BOND : bond 0.00306 ( 7) SS BOND : angle 1.12392 ( 14) hydrogen bonds : bond 0.03691 ( 464) hydrogen bonds : angle 4.84045 ( 1359) metal coordination : bond 0.00188 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.7901 (ptmm) cc_final: 0.7571 (ptmm) REVERT: B 201 TYR cc_start: 0.8249 (t80) cc_final: 0.7868 (t80) REVERT: A 98 LEU cc_start: 0.9154 (mp) cc_final: 0.8895 (mp) REVERT: A 102 TYR cc_start: 0.8188 (t80) cc_final: 0.7932 (t80) REVERT: A 109 ASN cc_start: 0.7605 (p0) cc_final: 0.7297 (t0) REVERT: E 140 ASN cc_start: 0.8442 (m-40) cc_final: 0.8172 (m-40) REVERT: F 160 LYS cc_start: 0.8722 (tppt) cc_final: 0.7907 (tppt) REVERT: F 187 LEU cc_start: 0.8531 (tp) cc_final: 0.7897 (pp) REVERT: F 223 LYS cc_start: 0.8219 (mmpt) cc_final: 0.7587 (tppt) REVERT: D 111 ARG cc_start: 0.6867 (ptm-80) cc_final: 0.6155 (ttp80) REVERT: D 131 ASN cc_start: 0.6764 (m110) cc_final: 0.6559 (m110) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.0875 time to fit residues: 20.6674 Evaluate side-chains 129 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 91 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 98 optimal weight: 0.0070 chunk 20 optimal weight: 0.1980 chunk 60 optimal weight: 0.1980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.128741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.100651 restraints weight = 24630.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099286 restraints weight = 32648.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.100602 restraints weight = 25769.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.100979 restraints weight = 15981.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.102912 restraints weight = 13309.261| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10602 Z= 0.114 Angle : 0.572 6.738 14419 Z= 0.290 Chirality : 0.041 0.166 1678 Planarity : 0.004 0.067 1808 Dihedral : 4.068 21.833 1446 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.23), residues: 1323 helix: 1.50 (0.27), residues: 385 sheet: 0.27 (0.26), residues: 394 loop : -0.71 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 67 TYR 0.010 0.001 TYR D 98 PHE 0.022 0.001 PHE A 277 TRP 0.043 0.001 TRP E 95 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00261 (10585) covalent geometry : angle 0.57141 (14405) SS BOND : bond 0.00357 ( 7) SS BOND : angle 0.98072 ( 14) hydrogen bonds : bond 0.03509 ( 464) hydrogen bonds : angle 4.68419 ( 1359) metal coordination : bond 0.00100 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.7898 (ptmm) cc_final: 0.7570 (ptmm) REVERT: B 201 TYR cc_start: 0.8205 (t80) cc_final: 0.7893 (t80) REVERT: A 88 GLN cc_start: 0.8448 (pp30) cc_final: 0.7993 (pp30) REVERT: A 98 LEU cc_start: 0.9160 (mp) cc_final: 0.8877 (mp) REVERT: A 102 TYR cc_start: 0.8125 (t80) cc_final: 0.7908 (t80) REVERT: A 109 ASN cc_start: 0.7516 (p0) cc_final: 0.7268 (t0) REVERT: F 86 MET cc_start: 0.7810 (ttp) cc_final: 0.7598 (ttm) REVERT: F 160 LYS cc_start: 0.8710 (tppt) cc_final: 0.7902 (tppt) REVERT: F 187 LEU cc_start: 0.8531 (tp) cc_final: 0.7893 (pp) REVERT: F 223 LYS cc_start: 0.8169 (mmpt) cc_final: 0.7584 (tppt) REVERT: D 111 ARG cc_start: 0.6795 (ptm-80) cc_final: 0.6108 (ttp80) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.0920 time to fit residues: 21.6173 Evaluate side-chains 134 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 20 optimal weight: 0.0870 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 163 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.127024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.098169 restraints weight = 24805.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097632 restraints weight = 31943.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.098608 restraints weight = 22442.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.098701 restraints weight = 15385.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099936 restraints weight = 12683.142| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10602 Z= 0.152 Angle : 0.582 6.200 14419 Z= 0.299 Chirality : 0.042 0.167 1678 Planarity : 0.004 0.066 1808 Dihedral : 4.156 22.028 1446 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.23), residues: 1323 helix: 1.54 (0.26), residues: 385 sheet: 0.39 (0.27), residues: 376 loop : -0.81 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 67 TYR 0.014 0.001 TYR E 50 PHE 0.018 0.001 PHE A 277 TRP 0.041 0.002 TRP E 95 HIS 0.006 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00352 (10585) covalent geometry : angle 0.58089 (14405) SS BOND : bond 0.00315 ( 7) SS BOND : angle 1.09656 ( 14) hydrogen bonds : bond 0.03606 ( 464) hydrogen bonds : angle 4.77656 ( 1359) metal coordination : bond 0.00209 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1522.78 seconds wall clock time: 27 minutes 12.09 seconds (1632.09 seconds total)