Starting phenix.real_space_refine on Mon Jun 9 07:19:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6i_28884/06_2025/8f6i_28884.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6i_28884/06_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_28884/06_2025/8f6i_28884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6i_28884/06_2025/8f6i_28884.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6i_28884/06_2025/8f6i_28884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6i_28884/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.88, per 1000 atoms: 0.66 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: 2.54 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: 1.36 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: 3.32 Time building geometry restraints manager: 3.03 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: 22.240 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.410 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.870 ------------------------------------------------------------------------------- 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 : 7.30 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 Details of bonding type rmsd hydrogen bonds : bond 0.29427 ( 464) hydrogen bonds : angle 9.20416 ( 1359) metal coordination : bond 0.00287 ( 10) SS BOND : bond 0.00159 ( 7) SS BOND : angle 0.52833 ( 14) covalent geometry : bond 0.00216 (10585) covalent geometry : angle 0.50426 (14405) *********************** 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 : 1.201 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: 0.2163 time to fit residues: 47.9997 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 : 1.289 ------------------------------------------------------------------------------- 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: 10.0000 chunk 53 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 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 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 = 0.3843 r_free = 0.3843 target = 0.125215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.096153 restraints weight = 25117.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.094555 restraints weight = 32883.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.095815 restraints weight = 25644.091| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 10602 Z= 0.231 Angle : 0.623 9.319 14419 Z= 0.333 Chirality : 0.043 0.154 1678 Planarity : 0.004 0.046 1808 Dihedral : 4.199 24.223 1446 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.05 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % 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: 0.22 (0.23), residues: 1323 helix: 1.53 (0.27), residues: 388 sheet: 0.33 (0.27), residues: 368 loop : -0.93 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 95 HIS 0.008 0.001 HIS A 250 PHE 0.026 0.002 PHE A 249 TYR 0.018 0.002 TYR F 193 ARG 0.005 0.001 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.06387 ( 464) hydrogen bonds : angle 6.03468 ( 1359) metal coordination : bond 0.00291 ( 10) SS BOND : bond 0.00228 ( 7) SS BOND : angle 0.89390 ( 14) covalent geometry : bond 0.00515 (10585) covalent geometry : angle 0.62258 (14405) *********************** 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 170 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7211 (t-100) cc_final: 0.6648 (t-100) REVERT: A 88 GLN cc_start: 0.8610 (pp30) cc_final: 0.8177 (pp30) REVERT: A 274 LYS cc_start: 0.9186 (ttmt) cc_final: 0.8963 (ttmm) REVERT: E 91 GLN cc_start: 0.9028 (pp30) cc_final: 0.8597 (pp30) REVERT: E 140 ASN cc_start: 0.8577 (m-40) cc_final: 0.8304 (m-40) REVERT: D 118 MET cc_start: 0.8571 (mtt) cc_final: 0.8187 (mtt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2598 time to fit residues: 63.3293 Evaluate side-chains 123 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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: 0.8980 chunk 4 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** ** D 131 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 = 0.3851 r_free = 0.3851 target = 0.125749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.096386 restraints weight = 25372.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.095479 restraints weight = 31866.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.096484 restraints weight = 22964.642| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10602 Z= 0.178 Angle : 0.584 7.907 14419 Z= 0.306 Chirality : 0.042 0.175 1678 Planarity : 0.004 0.063 1808 Dihedral : 4.211 22.310 1446 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.71 % Rotamer: Outliers : 0.09 % Allowed : 5.20 % Favored : 94.71 % 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: 0.15 (0.23), residues: 1323 helix: 1.51 (0.26), residues: 390 sheet: 0.21 (0.27), residues: 362 loop : -0.95 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 95 HIS 0.006 0.001 HIS A 250 PHE 0.019 0.001 PHE A 249 TYR 0.013 0.001 TYR E 50 ARG 0.009 0.000 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.05306 ( 464) hydrogen bonds : angle 5.56484 ( 1359) metal coordination : bond 0.00220 ( 10) SS BOND : bond 0.00407 ( 7) SS BOND : angle 0.89139 ( 14) covalent geometry : bond 0.00397 (10585) covalent geometry : angle 0.58390 (14405) *********************** 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 171 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 1.202 Fit side-chains REVERT: A 88 GLN cc_start: 0.8610 (pp30) cc_final: 0.8165 (pp30) REVERT: A 168 LEU cc_start: 0.9029 (pp) cc_final: 0.8810 (mt) REVERT: A 274 LYS cc_start: 0.9189 (ttmt) cc_final: 0.8973 (ttmm) REVERT: E 5 MET cc_start: 0.9008 (mmt) cc_final: 0.8633 (mmm) REVERT: E 91 GLN cc_start: 0.8892 (pp30) cc_final: 0.8467 (pp30) REVERT: E 95 TRP cc_start: 0.8331 (OUTLIER) cc_final: 0.8077 (t60) REVERT: E 140 ASN cc_start: 0.8623 (m-40) cc_final: 0.8378 (m-40) REVERT: F 160 LYS cc_start: 0.8740 (tppt) cc_final: 0.7963 (tppt) REVERT: F 223 LYS cc_start: 0.8575 (tppt) cc_final: 0.8230 (mmtt) REVERT: C 94 SER cc_start: 0.9117 (m) cc_final: 0.8654 (p) REVERT: D 118 MET cc_start: 0.8518 (mtt) cc_final: 0.8278 (mtt) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.2944 time to fit residues: 73.4194 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 : 1.826 ------------------------------------------------------------------------------- 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: 3.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 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 205 GLN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.124965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.095908 restraints weight = 25015.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.094876 restraints weight = 31775.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.095828 restraints weight = 22833.207| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 10602 Z= 0.200 Angle : 0.599 7.857 14419 Z= 0.313 Chirality : 0.043 0.153 1678 Planarity : 0.004 0.062 1808 Dihedral : 4.330 22.091 1446 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.20 % Favored : 93.65 % 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 (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: -0.00 (0.23), residues: 1323 helix: 1.42 (0.26), residues: 389 sheet: 0.13 (0.27), residues: 368 loop : -1.08 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 95 HIS 0.011 0.001 HIS A 250 PHE 0.011 0.001 PHE A 249 TYR 0.016 0.001 TYR E 50 ARG 0.006 0.000 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.04789 ( 464) hydrogen bonds : angle 5.39865 ( 1359) metal coordination : bond 0.00686 ( 10) SS BOND : bond 0.00271 ( 7) SS BOND : angle 1.36332 ( 14) covalent geometry : bond 0.00455 (10585) covalent geometry : angle 0.59825 (14405) *********************** 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 169 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8673 (pp30) cc_final: 0.7997 (pp30) REVERT: A 102 TYR cc_start: 0.8374 (t80) cc_final: 0.8114 (t80) REVERT: A 191 TYR cc_start: 0.7987 (t80) cc_final: 0.7767 (t80) REVERT: A 274 LYS cc_start: 0.9186 (ttmt) cc_final: 0.8982 (ttmm) REVERT: E 91 GLN cc_start: 0.8976 (pp30) cc_final: 0.8517 (pp30) REVERT: E 96 PRO cc_start: 0.8780 (Cg_exo) cc_final: 0.8494 (Cg_endo) REVERT: E 119 ILE cc_start: 0.7503 (mp) cc_final: 0.7053 (pt) REVERT: E 140 ASN cc_start: 0.8662 (m-40) cc_final: 0.8316 (m-40) REVERT: F 160 LYS cc_start: 0.8773 (tppt) cc_final: 0.7926 (tppt) REVERT: C 94 SER cc_start: 0.8918 (m) cc_final: 0.8697 (p) REVERT: D 131 ASN cc_start: 0.6948 (m110) cc_final: 0.6697 (m110) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2264 time to fit residues: 54.4737 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 : 1.608 ------------------------------------------------------------------------------- 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: 0.4980 chunk 89 optimal weight: 0.1980 chunk 124 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 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 58 ASN ** 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 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 = 0.126266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096474 restraints weight = 24801.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.096426 restraints weight = 28828.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.097062 restraints weight = 23540.508| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10602 Z= 0.143 Angle : 0.567 7.005 14419 Z= 0.294 Chirality : 0.042 0.158 1678 Planarity : 0.004 0.059 1808 Dihedral : 4.244 26.114 1446 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.37 % Favored : 94.48 % 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: 0.10 (0.23), residues: 1323 helix: 1.49 (0.26), residues: 388 sheet: 0.16 (0.27), residues: 372 loop : -0.98 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 95 HIS 0.009 0.001 HIS B 285 PHE 0.014 0.001 PHE A 49 TYR 0.011 0.001 TYR D 98 ARG 0.007 0.001 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 464) hydrogen bonds : angle 5.15504 ( 1359) metal coordination : bond 0.00419 ( 10) SS BOND : bond 0.00315 ( 7) SS BOND : angle 0.88256 ( 14) covalent geometry : bond 0.00324 (10585) covalent geometry : angle 0.56627 (14405) *********************** 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 174 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 201 TYR cc_start: 0.8242 (t80) cc_final: 0.7723 (t80) REVERT: A 88 GLN cc_start: 0.8660 (pp30) cc_final: 0.7918 (pp30) REVERT: A 102 TYR cc_start: 0.8387 (t80) cc_final: 0.8004 (t80) REVERT: A 191 TYR cc_start: 0.7907 (t80) cc_final: 0.7698 (t80) REVERT: A 274 LYS cc_start: 0.9177 (ttmt) cc_final: 0.8973 (ttmm) REVERT: E 119 ILE cc_start: 0.7408 (mp) cc_final: 0.7037 (pt) REVERT: E 140 ASN cc_start: 0.8585 (m-40) cc_final: 0.8363 (m-40) REVERT: F 160 LYS cc_start: 0.8766 (tppt) cc_final: 0.7812 (tppt) REVERT: F 161 ASP cc_start: 0.7911 (m-30) cc_final: 0.7680 (m-30) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2428 time to fit residues: 60.0318 Evaluate side-chains 136 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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: 1.9990 chunk 19 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 122 optimal weight: 0.0270 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.125359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.095953 restraints weight = 25133.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097996 restraints weight = 32250.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.097850 restraints weight = 21477.110| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 10602 Z= 0.181 Angle : 0.592 6.840 14419 Z= 0.308 Chirality : 0.043 0.173 1678 Planarity : 0.004 0.072 1808 Dihedral : 4.334 26.959 1446 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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: 1.53 (0.26), residues: 388 sheet: 0.17 (0.27), residues: 371 loop : -1.03 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 95 HIS 0.006 0.001 HIS B 285 PHE 0.021 0.001 PHE A 49 TYR 0.016 0.001 TYR C 37 ARG 0.006 0.000 ARG E 144 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 464) hydrogen bonds : angle 5.12812 ( 1359) metal coordination : bond 0.00235 ( 10) SS BOND : bond 0.00352 ( 7) SS BOND : angle 0.92594 ( 14) covalent geometry : bond 0.00413 (10585) covalent geometry : angle 0.59171 (14405) *********************** 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 171 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: B 201 TYR cc_start: 0.8059 (t80) cc_final: 0.7634 (t80) REVERT: A 88 GLN cc_start: 0.8611 (pp30) cc_final: 0.7948 (pp30) REVERT: A 102 TYR cc_start: 0.8182 (t80) cc_final: 0.7943 (t80) REVERT: A 274 LYS cc_start: 0.9183 (ttmt) cc_final: 0.8983 (ttmm) REVERT: E 91 GLN cc_start: 0.9101 (pp30) cc_final: 0.8618 (pp30) REVERT: E 119 ILE cc_start: 0.7289 (mp) cc_final: 0.6895 (pt) REVERT: E 140 ASN cc_start: 0.8653 (m-40) cc_final: 0.8324 (m-40) REVERT: F 160 LYS cc_start: 0.8748 (tppt) cc_final: 0.7850 (tppt) REVERT: D 131 ASN cc_start: 0.6960 (m110) cc_final: 0.6675 (m110) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2615 time to fit residues: 62.9598 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 : 1.232 ------------------------------------------------------------------------------- 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: 6.9990 chunk 21 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 123 optimal weight: 0.4980 chunk 39 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 ** F 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** 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 = 0.3854 r_free = 0.3854 target = 0.125994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.097343 restraints weight = 25294.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.095707 restraints weight = 33369.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.096898 restraints weight = 24356.792| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10602 Z= 0.157 Angle : 0.585 6.481 14419 Z= 0.303 Chirality : 0.043 0.166 1678 Planarity : 0.004 0.073 1808 Dihedral : 4.289 24.192 1446 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.09 % Allowed : 1.23 % Favored : 98.68 % 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: 0.11 (0.23), residues: 1323 helix: 1.50 (0.26), residues: 385 sheet: 0.18 (0.27), residues: 372 loop : -0.97 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 95 HIS 0.006 0.001 HIS A 250 PHE 0.011 0.001 PHE B 49 TYR 0.024 0.001 TYR A 156 ARG 0.004 0.000 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 464) hydrogen bonds : angle 5.01058 ( 1359) metal coordination : bond 0.00228 ( 10) SS BOND : bond 0.00506 ( 7) SS BOND : angle 1.17802 ( 14) covalent geometry : bond 0.00359 (10585) covalent geometry : angle 0.58419 (14405) *********************** 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 167 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: B 201 TYR cc_start: 0.8215 (t80) cc_final: 0.7768 (t80) REVERT: A 88 GLN cc_start: 0.8668 (pp30) cc_final: 0.7904 (pp30) REVERT: A 102 TYR cc_start: 0.8385 (t80) cc_final: 0.8091 (t80) REVERT: E 140 ASN cc_start: 0.8679 (m-40) cc_final: 0.8475 (m-40) REVERT: F 160 LYS cc_start: 0.8773 (tppt) cc_final: 0.7818 (tppt) REVERT: F 223 LYS cc_start: 0.8595 (mmpt) cc_final: 0.8367 (mmpt) REVERT: D 131 ASN cc_start: 0.6947 (m110) cc_final: 0.6743 (m110) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.2412 time to fit residues: 57.9249 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 : 1.118 ------------------------------------------------------------------------------- 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: 6.9990 chunk 88 optimal weight: 0.0030 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 0.0370 chunk 56 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 overall best weight: 0.5068 ------------------------------------------------------------------------------- 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 ** 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 = 0.3878 r_free = 0.3878 target = 0.127626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.099568 restraints weight = 24914.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097625 restraints weight = 35475.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.099045 restraints weight = 25308.514| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10602 Z= 0.117 Angle : 0.584 7.380 14419 Z= 0.299 Chirality : 0.042 0.176 1678 Planarity : 0.004 0.074 1808 Dihedral : 4.208 25.728 1446 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.09 % Allowed : 1.15 % 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: 0.16 (0.23), residues: 1323 helix: 1.52 (0.26), residues: 385 sheet: 0.08 (0.26), residues: 391 loop : -0.84 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP E 95 HIS 0.004 0.001 HIS A 250 PHE 0.028 0.001 PHE A 49 TYR 0.012 0.001 TYR C 50 ARG 0.004 0.000 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 464) hydrogen bonds : angle 4.85367 ( 1359) metal coordination : bond 0.00144 ( 10) SS BOND : bond 0.00390 ( 7) SS BOND : angle 0.73918 ( 14) covalent geometry : bond 0.00259 (10585) covalent geometry : angle 0.58335 (14405) *********************** 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 168 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.7967 (ptmm) cc_final: 0.7609 (ptmm) REVERT: B 201 TYR cc_start: 0.8138 (t80) cc_final: 0.7766 (t80) REVERT: A 88 GLN cc_start: 0.8598 (pp30) cc_final: 0.7939 (pp30) REVERT: A 102 TYR cc_start: 0.8271 (t80) cc_final: 0.8043 (t80) REVERT: A 109 ASN cc_start: 0.7661 (p0) cc_final: 0.7406 (t0) REVERT: E 140 ASN cc_start: 0.8526 (m-40) cc_final: 0.8280 (m-40) REVERT: F 160 LYS cc_start: 0.8741 (tppt) cc_final: 0.7797 (tppt) REVERT: C 94 SER cc_start: 0.9028 (m) cc_final: 0.8489 (t) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.2190 time to fit residues: 52.4249 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 : 1.204 ------------------------------------------------------------------------------- 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: 7.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 6 optimal weight: 0.0970 chunk 101 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 58 optimal weight: 0.0670 overall best weight: 1.0120 ------------------------------------------------------------------------------- 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 ** 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 = 0.3869 r_free = 0.3869 target = 0.126845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.097594 restraints weight = 25176.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.096759 restraints weight = 31357.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097407 restraints weight = 24205.964| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10602 Z= 0.153 Angle : 0.589 6.446 14419 Z= 0.305 Chirality : 0.043 0.181 1678 Planarity : 0.004 0.075 1808 Dihedral : 4.247 26.292 1446 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % 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: 0.23 (0.23), residues: 1323 helix: 1.56 (0.26), residues: 385 sheet: 0.23 (0.27), residues: 382 loop : -0.87 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP E 95 HIS 0.007 0.001 HIS A 250 PHE 0.025 0.001 PHE A 277 TYR 0.013 0.001 TYR A 35 ARG 0.007 0.000 ARG E 144 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 464) hydrogen bonds : angle 4.86972 ( 1359) metal coordination : bond 0.00236 ( 10) SS BOND : bond 0.00354 ( 7) SS BOND : angle 1.30580 ( 14) covalent geometry : bond 0.00348 (10585) covalent geometry : angle 0.58766 (14405) *********************** 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 162 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8019 (ptmm) cc_final: 0.7694 (ptmm) REVERT: B 201 TYR cc_start: 0.8158 (t80) cc_final: 0.7787 (t80) REVERT: A 88 GLN cc_start: 0.8653 (pp30) cc_final: 0.7899 (pp30) REVERT: A 102 TYR cc_start: 0.8319 (t80) cc_final: 0.8106 (t80) REVERT: A 109 ASN cc_start: 0.7724 (p0) cc_final: 0.7456 (t0) REVERT: E 140 ASN cc_start: 0.8540 (m-40) cc_final: 0.8325 (m-40) REVERT: F 160 LYS cc_start: 0.8736 (tppt) cc_final: 0.7844 (tppt) REVERT: F 223 LYS cc_start: 0.8351 (mmpt) cc_final: 0.7956 (tppt) REVERT: C 94 SER cc_start: 0.9017 (m) cc_final: 0.8433 (t) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.2211 time to fit residues: 50.3924 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 : 1.082 ------------------------------------------------------------------------------- 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: 0.3980 chunk 122 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 94 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** 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 = 0.3880 r_free = 0.3880 target = 0.127717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.099090 restraints weight = 24931.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097126 restraints weight = 31393.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.098525 restraints weight = 24432.976| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3022 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= 0.126 Angle : 0.591 6.905 14419 Z= 0.302 Chirality : 0.042 0.191 1678 Planarity : 0.004 0.082 1808 Dihedral : 4.208 26.522 1446 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % 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: 0.19 (0.23), residues: 1323 helix: 1.55 (0.26), residues: 383 sheet: 0.15 (0.27), residues: 388 loop : -0.85 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 95 HIS 0.005 0.001 HIS A 250 PHE 0.022 0.001 PHE A 277 TYR 0.019 0.001 TYR F 55 ARG 0.004 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 464) hydrogen bonds : angle 4.72389 ( 1359) metal coordination : bond 0.00115 ( 10) SS BOND : bond 0.00360 ( 7) SS BOND : angle 1.21345 ( 14) covalent geometry : bond 0.00286 (10585) covalent geometry : angle 0.59001 (14405) ********************** 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 162 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8068 (ptmm) cc_final: 0.7727 (ptmm) REVERT: B 201 TYR cc_start: 0.8220 (t80) cc_final: 0.7893 (t80) REVERT: A 88 GLN cc_start: 0.8665 (pp30) cc_final: 0.8014 (pp30) REVERT: A 102 TYR cc_start: 0.8430 (t80) cc_final: 0.8174 (t80) REVERT: A 109 ASN cc_start: 0.7825 (p0) cc_final: 0.7558 (t0) REVERT: E 48 LEU cc_start: 0.9295 (mp) cc_final: 0.9010 (mp) REVERT: E 140 ASN cc_start: 0.8546 (m-40) cc_final: 0.8316 (m-40) REVERT: F 160 LYS cc_start: 0.8762 (tppt) cc_final: 0.7793 (tppt) REVERT: F 223 LYS cc_start: 0.8469 (mmpt) cc_final: 0.8047 (tppt) REVERT: C 94 SER cc_start: 0.9054 (m) cc_final: 0.8531 (t) REVERT: D 131 ASN cc_start: 0.6997 (m110) cc_final: 0.6790 (m110) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.2234 time to fit residues: 50.9026 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 : 1.511 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** F 216 ASN ** 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 = 0.3884 r_free = 0.3884 target = 0.127727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.098652 restraints weight = 24701.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097002 restraints weight = 30825.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098438 restraints weight = 26008.960| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10602 Z= 0.129 Angle : 0.592 6.716 14419 Z= 0.303 Chirality : 0.042 0.163 1678 Planarity : 0.004 0.082 1808 Dihedral : 4.177 26.638 1446 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.82 % 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: 0.25 (0.23), residues: 1323 helix: 1.57 (0.26), residues: 384 sheet: 0.18 (0.27), residues: 388 loop : -0.81 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 33 HIS 0.005 0.001 HIS A 250 PHE 0.019 0.001 PHE A 277 TYR 0.016 0.001 TYR F 55 ARG 0.008 0.001 ARG C 67 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 464) hydrogen bonds : angle 4.68294 ( 1359) metal coordination : bond 0.00124 ( 10) SS BOND : bond 0.00308 ( 7) SS BOND : angle 1.07238 ( 14) covalent geometry : bond 0.00295 (10585) covalent geometry : angle 0.59171 (14405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3450.17 seconds wall clock time: 62 minutes 21.99 seconds (3741.99 seconds total)