Starting phenix.real_space_refine on Fri Feb 14 16:07:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6i_28884/02_2025/8f6i_28884.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6i_28884/02_2025/8f6i_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_28884/02_2025/8f6i_28884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6i_28884/02_2025/8f6i_28884.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6i_28884/02_2025/8f6i_28884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6i_28884/02_2025/8f6i_28884.cif" } resolution = 4.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 7.17, per 1000 atoms: 0.69 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: 2.51 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.35 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: 3.26 Time building geometry restraints manager: 2.96 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 292 or resid 301 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: 2.190 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.170 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- 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 10585 Z= 0.141 Angle : 0.504 6.040 14405 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 : 7.30 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.029 0.001 TRP E 95 HIS 0.004 0.001 HIS A 250 PHE 0.018 0.001 PHE A 91 TYR 0.014 0.001 TYR F 193 ARG 0.005 0.000 ARG D 111 *********************** 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 : 1.136 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: 0.2137 time to fit residues: 47.5210 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 : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.126594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.097410 restraints weight = 25048.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.095878 restraints weight = 31632.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.097066 restraints weight = 24896.125| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10585 Z= 0.272 Angle : 0.588 7.551 14405 Z= 0.316 Chirality : 0.042 0.156 1678 Planarity : 0.004 0.045 1808 Dihedral : 3.992 24.340 1446 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.44 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.23), residues: 1323 helix: 1.58 (0.27), residues: 388 sheet: 0.46 (0.27), residues: 360 loop : -0.87 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 95 HIS 0.007 0.001 HIS A 250 PHE 0.021 0.001 PHE A 249 TYR 0.016 0.001 TYR F 193 ARG 0.004 0.000 ARG D 111 *********************** 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 : 1.255 Fit side-chains REVERT: B 79 LYS cc_start: 0.7898 (ptmm) cc_final: 0.7572 (ptmm) REVERT: B 98 LEU cc_start: 0.9611 (tp) cc_final: 0.9407 (tp) REVERT: A 33 TRP cc_start: 0.7120 (t-100) cc_final: 0.6589 (t-100) REVERT: A 88 GLN cc_start: 0.8583 (pp30) cc_final: 0.8163 (pp30) REVERT: A 274 LYS cc_start: 0.9180 (ttmt) cc_final: 0.8967 (ttmm) REVERT: E 91 GLN cc_start: 0.8905 (pp30) cc_final: 0.8485 (pp30) REVERT: E 140 ASN cc_start: 0.8505 (m-40) cc_final: 0.8267 (m-40) REVERT: C 95 TRP cc_start: 0.7825 (t60) cc_final: 0.6806 (t60) REVERT: D 80 ASN cc_start: 0.6210 (m-40) cc_final: 0.5970 (m-40) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2179 time to fit residues: 51.9472 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 : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN F 42 GLN ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.122470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.093824 restraints weight = 25471.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.091414 restraints weight = 37864.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.093075 restraints weight = 26270.202| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.131 10585 Z= 0.479 Angle : 0.697 9.547 14405 Z= 0.367 Chirality : 0.045 0.226 1678 Planarity : 0.005 0.065 1808 Dihedral : 4.669 21.602 1446 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.95 % Favored : 92.97 % Rotamer: Outliers : 0.09 % Allowed : 7.49 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1323 helix: 1.36 (0.26), residues: 390 sheet: -0.09 (0.26), residues: 382 loop : -1.18 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP E 95 HIS 0.010 0.002 HIS A 250 PHE 0.033 0.002 PHE A 249 TYR 0.020 0.002 TYR E 50 ARG 0.006 0.001 ARG C 62 *********************** 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 162 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7207 (t-100) cc_final: 0.6834 (t-100) REVERT: A 88 GLN cc_start: 0.8731 (pp30) cc_final: 0.8303 (pp30) REVERT: A 168 LEU cc_start: 0.9109 (pp) cc_final: 0.8856 (mt) REVERT: E 91 GLN cc_start: 0.9148 (pp30) cc_final: 0.8629 (pp30) REVERT: E 95 TRP cc_start: 0.8557 (OUTLIER) cc_final: 0.8166 (t60) REVERT: E 140 ASN cc_start: 0.8846 (m-40) cc_final: 0.8432 (m-40) REVERT: F 160 LYS cc_start: 0.8803 (tppt) cc_final: 0.7979 (tppt) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.2235 time to fit residues: 51.3593 Evaluate side-chains 127 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 73 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 106 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.3840 r_free = 0.3840 target = 0.125048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.096934 restraints weight = 24938.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.095054 restraints weight = 35128.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.096092 restraints weight = 28122.920| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10585 Z= 0.293 Angle : 0.609 7.556 14405 Z= 0.319 Chirality : 0.043 0.156 1678 Planarity : 0.004 0.064 1808 Dihedral : 4.470 24.636 1446 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.97 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.23), residues: 1323 helix: 1.40 (0.26), residues: 389 sheet: 0.03 (0.27), residues: 372 loop : -1.14 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 95 HIS 0.010 0.001 HIS A 250 PHE 0.012 0.001 PHE D 130 TYR 0.017 0.001 TYR E 50 ARG 0.008 0.001 ARG A 239 *********************** 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 167 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.6805 (t-100) cc_final: 0.6577 (t-100) REVERT: A 88 GLN cc_start: 0.8598 (pp30) cc_final: 0.7839 (pp30) REVERT: A 109 ASN cc_start: 0.7573 (p0) cc_final: 0.7258 (t0) REVERT: A 274 LYS cc_start: 0.9174 (ttmt) cc_final: 0.8966 (ttmm) REVERT: E 91 GLN cc_start: 0.8972 (pp30) cc_final: 0.8528 (pp30) REVERT: E 119 ILE cc_start: 0.7476 (mp) cc_final: 0.7030 (pt) REVERT: E 140 ASN cc_start: 0.8769 (m-40) cc_final: 0.8348 (m-40) REVERT: F 160 LYS cc_start: 0.8733 (tppt) cc_final: 0.7844 (tppt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2363 time to fit residues: 55.6397 Evaluate side-chains 130 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.124186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.095907 restraints weight = 24841.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.094420 restraints weight = 34984.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.095827 restraints weight = 26690.280| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 10585 Z= 0.302 Angle : 0.603 7.076 14405 Z= 0.315 Chirality : 0.043 0.187 1678 Planarity : 0.004 0.061 1808 Dihedral : 4.488 24.011 1446 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.50 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.23), residues: 1323 helix: 1.44 (0.26), residues: 386 sheet: 0.04 (0.27), residues: 371 loop : -1.09 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 33 HIS 0.006 0.001 HIS A 250 PHE 0.013 0.001 PHE D 130 TYR 0.015 0.001 TYR E 50 ARG 0.007 0.001 ARG B 210 *********************** 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 161 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 201 TYR cc_start: 0.8156 (t80) cc_final: 0.7648 (t80) REVERT: A 33 TRP cc_start: 0.6979 (t-100) cc_final: 0.6600 (t-100) REVERT: A 88 GLN cc_start: 0.8655 (pp30) cc_final: 0.7938 (pp30) REVERT: A 102 TYR cc_start: 0.8302 (t80) cc_final: 0.7988 (t80) REVERT: A 274 LYS cc_start: 0.9147 (ttmt) cc_final: 0.8942 (ttmm) REVERT: E 91 GLN cc_start: 0.9103 (pp30) cc_final: 0.8603 (pp30) REVERT: E 96 PRO cc_start: 0.8660 (Cg_exo) cc_final: 0.8200 (Cg_endo) REVERT: E 119 ILE cc_start: 0.7421 (mp) cc_final: 0.7058 (pt) REVERT: E 140 ASN cc_start: 0.8829 (m-40) cc_final: 0.8394 (m-40) REVERT: F 160 LYS cc_start: 0.8780 (tppt) cc_final: 0.7887 (tppt) REVERT: F 161 ASP cc_start: 0.7896 (m-30) cc_final: 0.7689 (m-30) REVERT: C 94 SER cc_start: 0.9078 (m) cc_final: 0.8533 (t) REVERT: D 119 ASP cc_start: 0.8720 (p0) cc_final: 0.8502 (p0) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2147 time to fit residues: 49.1249 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 : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 58 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 105 optimal weight: 0.0870 chunk 23 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.126759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.098407 restraints weight = 25020.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096890 restraints weight = 33827.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097910 restraints weight = 25510.610| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10585 Z= 0.169 Angle : 0.573 6.793 14405 Z= 0.291 Chirality : 0.042 0.141 1678 Planarity : 0.004 0.062 1808 Dihedral : 4.268 21.879 1446 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.23), residues: 1323 helix: 1.43 (0.26), residues: 389 sheet: 0.15 (0.27), residues: 370 loop : -0.99 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 95 HIS 0.005 0.001 HIS A 155 PHE 0.018 0.001 PHE A 91 TYR 0.013 0.001 TYR C 88 ARG 0.005 0.000 ARG C 62 *********************** 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 173 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 TYR cc_start: 0.8162 (t80) cc_final: 0.7711 (t80) REVERT: A 88 GLN cc_start: 0.8622 (pp30) cc_final: 0.7850 (pp30) REVERT: A 102 TYR cc_start: 0.8269 (t80) cc_final: 0.7989 (t80) REVERT: E 91 GLN cc_start: 0.8999 (pp30) cc_final: 0.8535 (pp30) REVERT: E 96 PRO cc_start: 0.8397 (Cg_exo) cc_final: 0.8191 (Cg_endo) REVERT: E 119 ILE cc_start: 0.7208 (mp) cc_final: 0.6838 (pt) REVERT: F 160 LYS cc_start: 0.8738 (tppt) cc_final: 0.7804 (tppt) REVERT: F 161 ASP cc_start: 0.7866 (m-30) cc_final: 0.7660 (m-30) REVERT: C 94 SER cc_start: 0.8939 (m) cc_final: 0.8506 (t) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2356 time to fit residues: 56.6508 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 : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** 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 = 0.3855 r_free = 0.3855 target = 0.126084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.089859 restraints weight = 25346.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.088909 restraints weight = 16650.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.089139 restraints weight = 12618.847| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10585 Z= 0.214 Angle : 0.579 6.214 14405 Z= 0.300 Chirality : 0.042 0.160 1678 Planarity : 0.004 0.057 1808 Dihedral : 4.261 24.491 1446 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.23), residues: 1323 helix: 1.45 (0.26), residues: 391 sheet: 0.10 (0.26), residues: 382 loop : -0.90 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 33 HIS 0.006 0.001 HIS A 250 PHE 0.023 0.001 PHE A 161 TYR 0.012 0.001 TYR A 35 ARG 0.007 0.000 ARG E 144 *********************** 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 162 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 201 TYR cc_start: 0.8493 (t80) cc_final: 0.8051 (t80) REVERT: A 33 TRP cc_start: 0.7849 (t-100) cc_final: 0.7366 (t-100) REVERT: A 41 MET cc_start: 0.8703 (ppp) cc_final: 0.8355 (ppp) REVERT: A 88 GLN cc_start: 0.8869 (pp30) cc_final: 0.8220 (pp30) REVERT: A 102 TYR cc_start: 0.8775 (t80) cc_final: 0.8277 (t80) REVERT: A 109 ASN cc_start: 0.7873 (p0) cc_final: 0.7570 (t0) REVERT: A 191 TYR cc_start: 0.8374 (t80) cc_final: 0.8136 (t80) REVERT: F 160 LYS cc_start: 0.8834 (tppt) cc_final: 0.7831 (tppt) REVERT: F 161 ASP cc_start: 0.8148 (m-30) cc_final: 0.7891 (m-30) REVERT: C 94 SER cc_start: 0.9019 (m) cc_final: 0.8532 (t) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2288 time to fit residues: 51.8995 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 : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN D 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.126215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.097086 restraints weight = 25025.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.098290 restraints weight = 32359.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.098497 restraints weight = 22090.544| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10585 Z= 0.216 Angle : 0.585 7.346 14405 Z= 0.300 Chirality : 0.042 0.183 1678 Planarity : 0.004 0.073 1808 Dihedral : 4.266 23.242 1446 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.09 % Allowed : 1.06 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.23), residues: 1323 helix: 1.43 (0.26), residues: 391 sheet: 0.05 (0.27), residues: 380 loop : -0.84 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 95 HIS 0.006 0.001 HIS A 250 PHE 0.022 0.002 PHE A 277 TYR 0.011 0.001 TYR E 50 ARG 0.008 0.001 ARG D 111 *********************** 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 160 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 TYR cc_start: 0.8059 (t80) cc_final: 0.7641 (t80) REVERT: A 33 TRP cc_start: 0.7047 (t-100) cc_final: 0.6803 (t-100) REVERT: A 88 GLN cc_start: 0.8623 (pp30) cc_final: 0.7872 (pp30) REVERT: A 102 TYR cc_start: 0.8199 (t80) cc_final: 0.7973 (t80) REVERT: E 140 ASN cc_start: 0.8623 (m-40) cc_final: 0.7985 (m-40) REVERT: F 160 LYS cc_start: 0.8746 (tppt) cc_final: 0.7799 (tppt) REVERT: F 161 ASP cc_start: 0.7839 (m-30) cc_final: 0.7630 (m-30) REVERT: C 94 SER cc_start: 0.9003 (m) cc_final: 0.8510 (t) REVERT: D 131 ASN cc_start: 0.6992 (m110) cc_final: 0.6760 (m110) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.2367 time to fit residues: 52.8583 Evaluate side-chains 132 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 6 optimal weight: 0.0770 chunk 101 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 58 optimal weight: 0.0000 overall best weight: 0.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.127174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.098842 restraints weight = 25123.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.095877 restraints weight = 30375.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097264 restraints weight = 27277.664| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10585 Z= 0.194 Angle : 0.581 6.349 14405 Z= 0.298 Chirality : 0.042 0.201 1678 Planarity : 0.004 0.074 1808 Dihedral : 4.250 25.298 1446 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.09 % Allowed : 0.79 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.23), residues: 1323 helix: 1.49 (0.26), residues: 390 sheet: 0.03 (0.27), residues: 390 loop : -0.86 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP E 95 HIS 0.005 0.001 HIS A 250 PHE 0.024 0.001 PHE B 97 TYR 0.014 0.001 TYR A 35 ARG 0.007 0.000 ARG E 144 *********************** 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 161 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 TYR cc_start: 0.8282 (t80) cc_final: 0.7899 (t80) REVERT: A 33 TRP cc_start: 0.7362 (t-100) cc_final: 0.6990 (t-100) REVERT: A 88 GLN cc_start: 0.8706 (pp30) cc_final: 0.8150 (pp30) REVERT: A 102 TYR cc_start: 0.8463 (t80) cc_final: 0.8139 (t80) REVERT: E 48 LEU cc_start: 0.9365 (mp) cc_final: 0.9025 (mp) REVERT: E 140 ASN cc_start: 0.8652 (m-40) cc_final: 0.8070 (m-40) REVERT: F 160 LYS cc_start: 0.8762 (tppt) cc_final: 0.7807 (tppt) REVERT: C 94 SER cc_start: 0.9046 (m) cc_final: 0.8551 (t) REVERT: D 111 ARG cc_start: 0.6500 (tmm160) cc_final: 0.6138 (ttp80) outliers start: 1 outliers final: 1 residues processed: 160 average time/residue: 0.2284 time to fit residues: 52.2002 Evaluate side-chains 131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 51 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.126771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.097550 restraints weight = 24929.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.096051 restraints weight = 31325.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.096997 restraints weight = 24148.976| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10585 Z= 0.208 Angle : 0.597 7.101 14405 Z= 0.304 Chirality : 0.043 0.206 1678 Planarity : 0.004 0.079 1808 Dihedral : 4.273 26.318 1446 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1323 helix: 1.49 (0.26), residues: 386 sheet: 0.09 (0.27), residues: 388 loop : -0.86 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP E 95 HIS 0.006 0.001 HIS A 250 PHE 0.038 0.002 PHE B 97 TYR 0.011 0.001 TYR D 98 ARG 0.007 0.000 ARG E 144 ********************** 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 161 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 TYR cc_start: 0.8195 (t80) cc_final: 0.7810 (t80) REVERT: A 33 TRP cc_start: 0.7227 (t-100) cc_final: 0.6958 (t-100) REVERT: A 88 GLN cc_start: 0.8651 (pp30) cc_final: 0.8105 (pp30) REVERT: A 102 TYR cc_start: 0.8329 (t80) cc_final: 0.8058 (t80) REVERT: A 109 ASN cc_start: 0.7733 (p0) cc_final: 0.7526 (t0) REVERT: E 140 ASN cc_start: 0.8599 (m-40) cc_final: 0.7970 (m-40) REVERT: F 86 MET cc_start: 0.7779 (ttp) cc_final: 0.7471 (ttm) REVERT: F 160 LYS cc_start: 0.8785 (tppt) cc_final: 0.7866 (tppt) REVERT: F 161 ASP cc_start: 0.7900 (m-30) cc_final: 0.7688 (m-30) REVERT: C 94 SER cc_start: 0.8988 (m) cc_final: 0.8481 (t) REVERT: D 131 ASN cc_start: 0.7141 (m110) cc_final: 0.6900 (m110) outliers start: 1 outliers final: 1 residues processed: 160 average time/residue: 0.2232 time to fit residues: 50.6201 Evaluate side-chains 136 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 119 optimal weight: 0.0870 chunk 21 optimal weight: 0.6980 chunk 66 optimal weight: 0.0050 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.9576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN D 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.126849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.098313 restraints weight = 24697.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.096561 restraints weight = 32529.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.098059 restraints weight = 25322.245| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10585 Z= 0.220 Angle : 0.602 6.559 14405 Z= 0.308 Chirality : 0.043 0.168 1678 Planarity : 0.004 0.077 1808 Dihedral : 4.285 25.899 1446 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.23), residues: 1323 helix: 1.51 (0.26), residues: 390 sheet: 0.16 (0.27), residues: 382 loop : -0.87 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP E 95 HIS 0.006 0.001 HIS A 250 PHE 0.016 0.001 PHE A 277 TYR 0.025 0.001 TYR A 156 ARG 0.007 0.000 ARG E 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2938.93 seconds wall clock time: 53 minutes 50.70 seconds (3230.70 seconds total)