Starting phenix.real_space_refine on Fri Sep 11 17:04:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f6j_28885/09_2026/8f6j_28885.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6j_28885/09_2026/8f6j_28885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8f6j_28885/09_2026/8f6j_28885.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f6j_28885/09_2026/8f6j_28885.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f6j_28885/09_2026/8f6j_28885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6j_28885/09_2026/8f6j_28885.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6j_28885/09_2026/8f6j_28885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6j_28885/09_2026/8f6j_28885.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 8 6.06 5 S 28 5.16 5 C 6676 2.51 5 N 1760 2.21 5 O 2000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10472 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2169 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 6, 'TRANS': 275} 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: "A" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2169 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 6, 'TRANS': 275} 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: 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: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.55, per 1000 atoms: 0.24 Number of scatterers: 10472 At special positions: 0 Unit cell: (67.977, 156.455, 145.665, 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 8 29.99 S 28 16.00 O 2000 8.00 N 1760 7.00 C 6676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, 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 F 157 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 213 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 390.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 250 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 234 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" ND1 HIS A 73 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 77 " pdb=" ZN A 304 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS A 263 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS B 285 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 250 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 234 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 77 " pdb="ZN ZN B 302 " - pdb=" ND1 HIS B 73 " pdb=" ZN B 304 " pdb="ZN ZN B 304 " - pdb=" NE2 HIS B 263 " pdb="ZN ZN B 304 " - pdb=" NE2 HIS A 285 " 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 24 sheets defined 33.1% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 12 through 34 removed outlier: 3.510A pdb=" N ARG B 16 " --> pdb=" O LYS B 12 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 41 through 67 removed outlier: 3.721A pdb=" N LEU B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 109 removed outlier: 4.484A pdb=" N ALA B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 142 removed outlier: 3.807A pdb=" N VAL B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 149 removed outlier: 3.632A pdb=" N VAL B 149 " --> pdb=" O SER B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 150 through 174 removed outlier: 3.791A pdb=" N HIS B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 178 through 208 removed outlier: 4.101A pdb=" N GLY B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 183 " --> pdb=" O TRP B 179 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN B 195 " --> pdb=" O TYR B 191 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 225 removed outlier: 3.595A pdb=" N LYS B 221 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.568A pdb=" N ILE B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 129 Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'F' and resid 90 through 94 removed outlier: 4.085A pdb=" N THR F 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing helix chain 'A' and resid 12 through 34 removed outlier: 3.522A pdb=" N THR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 67 removed outlier: 3.561A pdb=" N LEU A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 103 removed outlier: 4.470A pdb=" N ALA A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 95 " --> pdb=" O PHE A 91 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.958A pdb=" N ASN A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 141 removed outlier: 3.783A pdb=" N VAL A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 149 removed outlier: 3.564A pdb=" N VAL A 149 " --> pdb=" O SER A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 149' Processing helix chain 'A' and resid 150 through 175 removed outlier: 3.887A pdb=" N HIS A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 208 removed outlier: 4.220A pdb=" N ASP A 181 " --> pdb=" O TRP A 177 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 225 removed outlier: 3.593A pdb=" N LYS A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 removed outlier: 3.567A pdb=" N ILE A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.305A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 129 Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.517A pdb=" N GLU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 removed outlier: 4.076A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing sheet with id=AA1, first strand: chain 'B' and resid 233 through 240 removed outlier: 5.365A pdb=" N ASP B 235 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS B 250 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE B 249 " --> pdb=" O ILE B 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AA3, first strand: chain 'E' and resid 12 through 14 Processing sheet with id=AA4, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.807A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.053A pdb=" N ILE E 92 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR E 99 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER E 94 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 116 through 120 removed outlier: 3.644A pdb=" N SER E 116 " --> pdb=" O ASN E 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN E 139 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 134 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR E 175 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 178 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 6 through 10 removed outlier: 3.675A pdb=" N VAL F 8 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU F 21 " --> pdb=" O MET F 86 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU F 23 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 61 through 63 removed outlier: 5.649A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA F 52 " --> pdb=" O TRP F 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 106 through 107 Processing sheet with id=AB1, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.526A pdb=" N LEU F 158 " --> pdb=" O PHE F 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU F 141 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.526A pdb=" N LEU F 158 " --> pdb=" O PHE F 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU F 141 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 168 through 171 removed outlier: 3.694A pdb=" N THR F 168 " --> pdb=" O ASN F 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 233 through 240 removed outlier: 5.367A pdb=" N ASP A 235 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS A 250 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 249 " --> pdb=" O ILE A 283 " (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 12 through 14 Processing sheet with id=AB7, first strand: chain 'C' and resid 46 through 49 removed outlier: 5.801A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.052A pdb=" N ILE C 92 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N THR C 99 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER C 94 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.661A pdb=" N SER C 116 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN C 139 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 134 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR C 175 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 178 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.519A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 21 " --> pdb=" O MET D 86 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 23 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 61 through 63 removed outlier: 5.645A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AC4, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.513A pdb=" N LEU D 158 " --> pdb=" O PHE D 139 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 141 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY D 156 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.513A pdb=" N LEU D 158 " --> pdb=" O PHE D 139 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 141 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY D 156 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 168 through 171 removed outlier: 3.683A pdb=" N THR D 168 " --> pdb=" O ASN D 216 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.15 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: 3344 1.34 - 1.46: 2301 1.46 - 1.58: 5009 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 10692 Sorted by residual: bond pdb=" CB PRO F 184 " pdb=" CG PRO F 184 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.81e+00 bond pdb=" CB PRO D 184 " pdb=" CG PRO D 184 " ideal model delta sigma weight residual 1.492 1.549 -0.057 5.00e-02 4.00e+02 1.29e+00 bond pdb=" CG PRO F 184 " pdb=" CD PRO F 184 " ideal model delta sigma weight residual 1.503 1.541 -0.038 3.40e-02 8.65e+02 1.23e+00 bond pdb=" CB PRO E 81 " pdb=" CG PRO E 81 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.69e-01 bond pdb=" CG PRO C 143 " pdb=" CD PRO C 143 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.70e-02 1.37e+03 7.60e-01 ... (remaining 10687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 14148 1.32 - 2.63: 317 2.63 - 3.95: 63 3.95 - 5.27: 21 5.27 - 6.58: 5 Bond angle restraints: 14554 Sorted by residual: angle pdb=" CA PRO F 184 " pdb=" N PRO F 184 " pdb=" CD PRO F 184 " ideal model delta sigma weight residual 112.00 106.90 5.10 1.40e+00 5.10e-01 1.33e+01 angle pdb=" CA PRO D 184 " pdb=" N PRO D 184 " pdb=" CD PRO D 184 " ideal model delta sigma weight residual 112.00 108.79 3.21 1.40e+00 5.10e-01 5.26e+00 angle pdb=" CA LYS A 157 " pdb=" CB LYS A 157 " pdb=" CG LYS A 157 " ideal model delta sigma weight residual 114.10 118.63 -4.53 2.00e+00 2.50e-01 5.12e+00 angle pdb=" CB ARG A 202 " pdb=" CG ARG A 202 " pdb=" CD ARG A 202 " ideal model delta sigma weight residual 111.30 116.36 -5.06 2.30e+00 1.89e-01 4.83e+00 angle pdb=" C GLU E 189 " pdb=" N LYS E 190 " pdb=" CA LYS E 190 " ideal model delta sigma weight residual 121.54 125.66 -4.12 1.91e+00 2.74e-01 4.66e+00 ... (remaining 14549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5735 17.87 - 35.74: 485 35.74 - 53.61: 112 53.61 - 71.48: 9 71.48 - 89.35: 13 Dihedral angle restraints: 6354 sinusoidal: 2380 harmonic: 3974 Sorted by residual: 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 93.00 138.65 -45.65 1 1.00e+01 1.00e-02 2.89e+01 dihedral pdb=" CB CYS E 24 " pdb=" SG CYS E 24 " pdb=" SG CYS E 89 " pdb=" CB CYS E 89 " ideal model delta sinusoidal sigma weight residual 93.00 138.26 -45.26 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CA SER E 61 " pdb=" C SER E 61 " pdb=" N ARG E 62 " pdb=" CA ARG E 62 " ideal model delta harmonic sigma weight residual -180.00 -155.06 -24.94 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 6351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1088 0.031 - 0.062: 423 0.062 - 0.093: 106 0.093 - 0.125: 71 0.125 - 0.156: 6 Chirality restraints: 1694 Sorted by residual: chirality pdb=" CA PRO E 81 " pdb=" N PRO E 81 " pdb=" C PRO E 81 " pdb=" CB PRO E 81 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CA ILE E 49 " pdb=" N ILE E 49 " pdb=" C ILE E 49 " pdb=" CB ILE E 49 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 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 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 1691 not shown) Planarity restraints: 1832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE F 183 " 0.073 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO F 184 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO F 184 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO F 184 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 183 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.85e+01 pdb=" N PRO D 184 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO D 184 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO D 184 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 80 " 0.055 5.00e-02 4.00e+02 8.16e-02 1.06e+01 pdb=" N PRO E 81 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO E 81 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 81 " 0.045 5.00e-02 4.00e+02 ... (remaining 1829 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 152 2.65 - 3.21: 9666 3.21 - 3.77: 15296 3.77 - 4.34: 20644 4.34 - 4.90: 34157 Nonbonded interactions: 79915 Sorted by model distance: nonbonded pdb=" OD2 ASP A 70 " pdb="ZN ZN A 302 " model vdw 2.084 2.230 nonbonded pdb=" OD2 ASP B 70 " pdb="ZN ZN B 302 " model vdw 2.086 2.230 nonbonded pdb=" OD2 ASP A 159 " pdb="ZN ZN A 303 " model vdw 2.140 2.230 nonbonded pdb=" OD2 ASP B 159 " pdb="ZN ZN B 303 " model vdw 2.143 2.230 nonbonded pdb=" O PHE A 49 " pdb=" OG1 THR A 52 " model vdw 2.162 3.040 ... (remaining 79910 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.880 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.003 0.084 10712 Z= 0.114 Angle : 0.514 6.581 14570 Z= 0.260 Chirality : 0.040 0.156 1694 Planarity : 0.005 0.108 1832 Dihedral : 14.392 89.354 3770 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.04 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.24), residues: 1342 helix: 0.33 (0.27), residues: 366 sheet: -0.11 (0.29), residues: 370 loop : -0.78 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 202 TYR 0.008 0.001 TYR E 50 PHE 0.022 0.001 PHE A 49 TRP 0.008 0.001 TRP D 113 HIS 0.002 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.11 (10692) covalent geometry : angle 0.51361 / 0.26 (14554) SS BOND : bond 0.00111 / 0.07 ( 8) SS BOND : angle 0.46570 / 0.26 ( 16) hydrogen bonds : bond 0.28216 / 19.30 ( 467) hydrogen bonds : angle 8.66310 / 6.40 ( 1296) metal coordination : bond 0.00124 / 0.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.523 Fit side-chains REVERT: A 41 MET cc_start: 0.7181 (pmm) cc_final: 0.6967 (pmm) REVERT: A 101 PHE cc_start: 0.8444 (t80) cc_final: 0.8113 (t80) REVERT: A 202 ARG cc_start: 0.8272 (pmt170) cc_final: 0.8005 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1037 time to fit residues: 26.2874 Evaluate side-chains 155 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 GLN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 ASN E 160 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.200289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.136080 restraints weight = 12497.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129654 restraints weight = 16631.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122737 restraints weight = 12751.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122687 restraints weight = 14484.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122879 restraints weight = 12732.851| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 10712 Z= 0.299 Angle : 0.694 9.316 14570 Z= 0.369 Chirality : 0.048 0.174 1694 Planarity : 0.006 0.078 1832 Dihedral : 4.646 25.262 1466 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.75 % Favored : 91.88 % Rotamer: Outliers : 1.31 % Allowed : 13.29 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.24), residues: 1342 helix: 0.31 (0.25), residues: 390 sheet: -0.47 (0.28), residues: 400 loop : -1.20 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 202 TYR 0.019 0.002 TYR D 162 PHE 0.017 0.002 PHE B 49 TRP 0.017 0.002 TRP F 50 HIS 0.006 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.30 (10692) covalent geometry : angle 0.69461 / 0.37 (14554) SS BOND : bond 0.00433 / 0.24 ( 8) SS BOND : angle 0.45758 / 0.25 ( 16) hydrogen bonds : bond 0.05834 / 3.92 ( 467) hydrogen bonds : angle 5.45838 / 4.03 ( 1296) metal coordination : bond 0.00454 / 0.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.397 Fit side-chains REVERT: B 101 PHE cc_start: 0.8106 (t80) cc_final: 0.7897 (t80) REVERT: F 193 TYR cc_start: 0.8475 (m-80) cc_final: 0.8180 (m-10) REVERT: F 226 LYS cc_start: 0.8123 (tppp) cc_final: 0.7705 (tptp) REVERT: A 101 PHE cc_start: 0.8262 (t80) cc_final: 0.8009 (t80) REVERT: D 193 TYR cc_start: 0.8453 (m-80) cc_final: 0.8173 (m-10) REVERT: D 226 LYS cc_start: 0.8178 (tppp) cc_final: 0.7782 (tptp) outliers start: 15 outliers final: 12 residues processed: 174 average time/residue: 0.1029 time to fit residues: 25.5834 Evaluate side-chains 159 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 216 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 122 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 133 optimal weight: 0.0070 chunk 102 optimal weight: 0.6980 chunk 69 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.204672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.162483 restraints weight = 12694.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.147367 restraints weight = 16519.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143800 restraints weight = 22448.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.143546 restraints weight = 22455.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143878 restraints weight = 18742.939| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10712 Z= 0.171 Angle : 0.589 9.323 14570 Z= 0.309 Chirality : 0.043 0.143 1694 Planarity : 0.004 0.065 1832 Dihedral : 4.439 25.386 1466 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.59 % Favored : 94.11 % Rotamer: Outliers : 2.01 % Allowed : 15.91 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.24), residues: 1342 helix: 0.59 (0.26), residues: 378 sheet: -0.47 (0.28), residues: 400 loop : -1.19 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 202 TYR 0.020 0.001 TYR C 142 PHE 0.019 0.002 PHE B 49 TRP 0.011 0.001 TRP F 39 HIS 0.004 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (10692) covalent geometry : angle 0.58914 / 0.31 (14554) SS BOND : bond 0.00314 / 0.20 ( 8) SS BOND : angle 0.50586 / 0.28 ( 16) hydrogen bonds : bond 0.04682 / 3.14 ( 467) hydrogen bonds : angle 4.90132 / 3.62 ( 1296) metal coordination : bond 0.00228 / 0.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.381 Fit side-chains REVERT: E 91 GLN cc_start: 0.8960 (pp30) cc_final: 0.8626 (pp30) REVERT: A 101 PHE cc_start: 0.7159 (t80) cc_final: 0.6746 (t80) REVERT: A 205 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7536 (mm-40) REVERT: C 91 GLN cc_start: 0.8895 (pp30) cc_final: 0.8487 (pp30) REVERT: C 169 ASP cc_start: 0.8024 (m-30) cc_final: 0.7673 (m-30) outliers start: 23 outliers final: 17 residues processed: 184 average time/residue: 0.1034 time to fit residues: 27.0602 Evaluate side-chains 175 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 216 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 95 optimal weight: 0.0870 chunk 59 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 127 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 61.8834 > 50:) chunk 36 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 0.0170 chunk 34 optimal weight: 0.0980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** E 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.206227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.143753 restraints weight = 12631.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143223 restraints weight = 18239.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.139477 restraints weight = 15413.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.136869 restraints weight = 16955.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.137503 restraints weight = 15119.392| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10712 Z= 0.117 Angle : 0.557 10.113 14570 Z= 0.288 Chirality : 0.042 0.230 1694 Planarity : 0.004 0.059 1832 Dihedral : 4.229 25.807 1466 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.44 % Favored : 94.26 % Rotamer: Outliers : 1.75 % Allowed : 18.53 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.24), residues: 1342 helix: 0.76 (0.26), residues: 380 sheet: -0.38 (0.27), residues: 398 loop : -1.16 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 202 TYR 0.017 0.001 TYR C 142 PHE 0.018 0.001 PHE A 49 TRP 0.010 0.001 TRP F 39 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (10692) covalent geometry : angle 0.55720 / 0.29 (14554) SS BOND : bond 0.00232 / 0.15 ( 8) SS BOND : angle 0.45016 / 0.27 ( 16) hydrogen bonds : bond 0.03948 / 2.66 ( 467) hydrogen bonds : angle 4.52156 / 3.33 ( 1296) metal coordination : bond 0.00090 / 0.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.377 Fit side-chains REVERT: B 99 LEU cc_start: 0.8016 (mt) cc_final: 0.7696 (mt) REVERT: B 202 ARG cc_start: 0.7266 (mtm-85) cc_final: 0.7059 (mtm180) REVERT: E 91 GLN cc_start: 0.8832 (pp30) cc_final: 0.8524 (pp30) REVERT: E 169 ASP cc_start: 0.8210 (m-30) cc_final: 0.7793 (m-30) REVERT: E 174 THR cc_start: 0.9017 (t) cc_final: 0.8674 (t) REVERT: F 162 TYR cc_start: 0.7924 (p90) cc_final: 0.7531 (p90) REVERT: F 226 LYS cc_start: 0.8220 (tptp) cc_final: 0.7780 (tptp) REVERT: C 91 GLN cc_start: 0.8819 (pp30) cc_final: 0.8504 (pp30) REVERT: C 169 ASP cc_start: 0.8197 (m-30) cc_final: 0.7802 (m-30) REVERT: D 162 TYR cc_start: 0.7975 (p90) cc_final: 0.7594 (p90) REVERT: D 226 LYS cc_start: 0.8332 (tptp) cc_final: 0.8075 (tptp) outliers start: 20 outliers final: 12 residues processed: 182 average time/residue: 0.0999 time to fit residues: 25.9567 Evaluate side-chains 170 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 223 LYS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.203760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.155135 restraints weight = 12608.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149764 restraints weight = 21639.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144129 restraints weight = 22728.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143565 restraints weight = 21634.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143780 restraints weight = 17344.864| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10712 Z= 0.186 Angle : 0.607 12.634 14570 Z= 0.312 Chirality : 0.043 0.215 1694 Planarity : 0.004 0.057 1832 Dihedral : 4.381 25.440 1466 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.23 % Favored : 92.47 % Rotamer: Outliers : 3.06 % Allowed : 19.76 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.24), residues: 1342 helix: 0.76 (0.26), residues: 378 sheet: -0.53 (0.27), residues: 402 loop : -1.18 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 106 TYR 0.013 0.001 TYR C 142 PHE 0.020 0.002 PHE A 97 TRP 0.019 0.002 TRP B 33 HIS 0.005 0.001 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (10692) covalent geometry : angle 0.60749 / 0.31 (14554) SS BOND : bond 0.00281 / 0.17 ( 8) SS BOND : angle 0.46010 / 0.26 ( 16) hydrogen bonds : bond 0.03933 / 2.64 ( 467) hydrogen bonds : angle 4.42853 / 3.26 ( 1296) metal coordination : bond 0.00303 / 0.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: B 205 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7602 (tp40) REVERT: E 91 GLN cc_start: 0.8771 (pp30) cc_final: 0.8460 (pp30) REVERT: F 92 GLU cc_start: 0.7832 (tp30) cc_final: 0.7606 (tp30) REVERT: C 91 GLN cc_start: 0.8739 (pp30) cc_final: 0.8403 (pp30) REVERT: D 92 GLU cc_start: 0.7803 (tp30) cc_final: 0.7581 (tp30) outliers start: 35 outliers final: 21 residues processed: 194 average time/residue: 0.1029 time to fit residues: 28.6403 Evaluate side-chains 180 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 197 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 110 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 129 optimal weight: 0.0570 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** 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 = 0.4353 r_free = 0.4353 target = 0.204524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.158010 restraints weight = 12682.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.150283 restraints weight = 20092.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.146324 restraints weight = 20899.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145702 restraints weight = 22165.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.144996 restraints weight = 18605.059| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10712 Z= 0.154 Angle : 0.594 10.145 14570 Z= 0.307 Chirality : 0.043 0.199 1694 Planarity : 0.004 0.055 1832 Dihedral : 4.335 25.351 1466 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.93 % Favored : 92.70 % Rotamer: Outliers : 2.62 % Allowed : 21.15 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1342 helix: 0.81 (0.26), residues: 380 sheet: -0.48 (0.27), residues: 402 loop : -1.15 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 106 TYR 0.013 0.001 TYR C 142 PHE 0.038 0.002 PHE A 101 TRP 0.017 0.002 TRP B 33 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (10692) covalent geometry : angle 0.59428 / 0.31 (14554) SS BOND : bond 0.00272 / 0.18 ( 8) SS BOND : angle 0.42463 / 0.24 ( 16) hydrogen bonds : bond 0.03649 / 2.45 ( 467) hydrogen bonds : angle 4.31365 / 3.16 ( 1296) metal coordination : bond 0.00198 / 0.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: E 91 GLN cc_start: 0.8798 (pp30) cc_final: 0.8426 (pp30) REVERT: E 169 ASP cc_start: 0.8038 (m-30) cc_final: 0.7730 (m-30) REVERT: A 141 LEU cc_start: 0.2165 (OUTLIER) cc_final: 0.1766 (mp) REVERT: C 91 GLN cc_start: 0.8805 (pp30) cc_final: 0.8436 (pp30) REVERT: C 169 ASP cc_start: 0.8054 (m-30) cc_final: 0.7761 (m-30) REVERT: D 226 LYS cc_start: 0.8358 (tppp) cc_final: 0.8096 (tptp) outliers start: 30 outliers final: 26 residues processed: 191 average time/residue: 0.1019 time to fit residues: 27.8047 Evaluate side-chains 188 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 197 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 chunk 32 optimal weight: 0.0970 chunk 11 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 89 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 73 optimal weight: 0.0270 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** E 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** 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 = 0.4373 r_free = 0.4373 target = 0.206826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.147474 restraints weight = 12490.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.145094 restraints weight = 19893.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141279 restraints weight = 18326.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140350 restraints weight = 19099.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141570 restraints weight = 16570.444| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10712 Z= 0.115 Angle : 0.591 13.277 14570 Z= 0.298 Chirality : 0.042 0.200 1694 Planarity : 0.004 0.053 1832 Dihedral : 4.150 25.599 1466 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.59 % Favored : 94.04 % Rotamer: Outliers : 2.36 % Allowed : 21.94 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.24), residues: 1342 helix: 0.98 (0.26), residues: 376 sheet: -0.35 (0.27), residues: 404 loop : -1.17 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 202 TYR 0.013 0.001 TYR C 142 PHE 0.037 0.002 PHE A 101 TRP 0.019 0.001 TRP B 33 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (10692) covalent geometry : angle 0.59090 / 0.30 (14554) SS BOND : bond 0.00239 / 0.15 ( 8) SS BOND : angle 0.40280 / 0.24 ( 16) hydrogen bonds : bond 0.03332 / 2.25 ( 467) hydrogen bonds : angle 4.16604 / 3.05 ( 1296) metal coordination : bond 0.00062 / 0.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: B 198 ASP cc_start: 0.7015 (t0) cc_final: 0.6699 (t0) REVERT: E 91 GLN cc_start: 0.8810 (pp30) cc_final: 0.8533 (pp30) REVERT: F 226 LYS cc_start: 0.8200 (tppp) cc_final: 0.7870 (tmtt) REVERT: A 141 LEU cc_start: 0.2417 (OUTLIER) cc_final: 0.1987 (mp) REVERT: C 91 GLN cc_start: 0.8856 (pp30) cc_final: 0.8559 (pp30) outliers start: 27 outliers final: 21 residues processed: 193 average time/residue: 0.1044 time to fit residues: 28.6980 Evaluate side-chains 189 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 129 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.205758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144584 restraints weight = 12572.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.140151 restraints weight = 18347.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.131691 restraints weight = 12551.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130012 restraints weight = 13860.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130860 restraints weight = 14566.454| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10712 Z= 0.135 Angle : 0.596 12.201 14570 Z= 0.302 Chirality : 0.043 0.199 1694 Planarity : 0.004 0.052 1832 Dihedral : 4.183 25.273 1466 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.26 % Favored : 93.37 % Rotamer: Outliers : 2.19 % Allowed : 22.81 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.24), residues: 1342 helix: 1.05 (0.27), residues: 376 sheet: -0.33 (0.27), residues: 402 loop : -1.23 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 202 TYR 0.023 0.001 TYR A 102 PHE 0.038 0.002 PHE A 101 TRP 0.017 0.001 TRP B 33 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (10692) covalent geometry : angle 0.59627 / 0.30 (14554) SS BOND : bond 0.00279 / 0.18 ( 8) SS BOND : angle 0.45467 / 0.26 ( 16) hydrogen bonds : bond 0.03375 / 2.26 ( 467) hydrogen bonds : angle 4.13473 / 3.04 ( 1296) metal coordination : bond 0.00148 / 0.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: B 207 LEU cc_start: 0.7778 (tt) cc_final: 0.7334 (tt) REVERT: E 91 GLN cc_start: 0.8829 (pp30) cc_final: 0.8511 (pp30) REVERT: E 163 GLU cc_start: 0.8126 (pm20) cc_final: 0.7841 (pm20) REVERT: F 226 LYS cc_start: 0.8054 (tppp) cc_final: 0.7553 (tmtt) REVERT: A 23 LEU cc_start: 0.8324 (tp) cc_final: 0.8045 (tt) REVERT: A 141 LEU cc_start: 0.2251 (OUTLIER) cc_final: 0.1843 (mp) REVERT: C 91 GLN cc_start: 0.8787 (pp30) cc_final: 0.8478 (pp30) outliers start: 25 outliers final: 22 residues processed: 189 average time/residue: 0.1019 time to fit residues: 27.4813 Evaluate side-chains 189 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.0000 chunk 5 optimal weight: 2.9990 chunk 115 optimal weight: 0.0070 chunk 122 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 ASN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN D 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.205763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147069 restraints weight = 12596.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145938 restraints weight = 21740.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.147563 restraints weight = 20286.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142427 restraints weight = 14442.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142935 restraints weight = 14881.816| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10712 Z= 0.135 Angle : 0.602 12.078 14570 Z= 0.302 Chirality : 0.042 0.193 1694 Planarity : 0.004 0.053 1832 Dihedral : 4.163 25.218 1466 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.96 % Favored : 93.67 % Rotamer: Outliers : 2.80 % Allowed : 22.64 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.24), residues: 1342 helix: 1.06 (0.27), residues: 376 sheet: -0.39 (0.27), residues: 404 loop : -1.20 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 106 TYR 0.027 0.001 TYR A 102 PHE 0.023 0.002 PHE A 97 TRP 0.019 0.001 TRP B 33 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (10692) covalent geometry : angle 0.60172 / 0.30 (14554) SS BOND : bond 0.00250 / 0.16 ( 8) SS BOND : angle 0.45858 / 0.26 ( 16) hydrogen bonds : bond 0.03271 / 2.20 ( 467) hydrogen bonds : angle 4.08633 / 2.98 ( 1296) metal coordination : bond 0.00149 / 0.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: B 198 ASP cc_start: 0.6979 (t0) cc_final: 0.6746 (t0) REVERT: E 91 GLN cc_start: 0.8728 (pp30) cc_final: 0.8405 (pp30) REVERT: A 23 LEU cc_start: 0.7800 (tp) cc_final: 0.7493 (tt) REVERT: A 141 LEU cc_start: 0.2574 (OUTLIER) cc_final: 0.2153 (mp) REVERT: C 91 GLN cc_start: 0.8801 (pp30) cc_final: 0.8485 (pp30) REVERT: C 163 GLU cc_start: 0.7915 (pm20) cc_final: 0.7650 (pt0) REVERT: D 226 LYS cc_start: 0.8414 (tppp) cc_final: 0.8098 (tptp) outliers start: 32 outliers final: 28 residues processed: 190 average time/residue: 0.0973 time to fit residues: 26.8900 Evaluate side-chains 192 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 41 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 25 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 GLN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.202868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.156434 restraints weight = 12526.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145401 restraints weight = 19906.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.142836 restraints weight = 19535.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.142891 restraints weight = 21416.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.140897 restraints weight = 17520.799| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10712 Z= 0.215 Angle : 0.649 11.797 14570 Z= 0.331 Chirality : 0.044 0.203 1694 Planarity : 0.004 0.053 1832 Dihedral : 4.399 24.823 1466 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.38 % Favored : 92.25 % Rotamer: Outliers : 2.71 % Allowed : 22.73 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.24), residues: 1342 helix: 0.96 (0.27), residues: 382 sheet: -0.50 (0.27), residues: 404 loop : -1.32 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 106 TYR 0.012 0.002 TYR A 102 PHE 0.034 0.002 PHE A 101 TRP 0.018 0.002 TRP B 33 HIS 0.005 0.001 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (10692) covalent geometry : angle 0.64941 / 0.33 (14554) SS BOND : bond 0.00304 / 0.19 ( 8) SS BOND : angle 0.53255 / 0.30 ( 16) hydrogen bonds : bond 0.03585 / 2.42 ( 467) hydrogen bonds : angle 4.18891 / 3.08 ( 1296) metal coordination : bond 0.00370 / 0.29 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: B 207 LEU cc_start: 0.7332 (tt) cc_final: 0.6818 (tt) REVERT: E 91 GLN cc_start: 0.8728 (pp30) cc_final: 0.8323 (pp30) REVERT: E 163 GLU cc_start: 0.7846 (pm20) cc_final: 0.7608 (pt0) REVERT: A 23 LEU cc_start: 0.7688 (tp) cc_final: 0.7371 (tt) REVERT: A 141 LEU cc_start: 0.2679 (OUTLIER) cc_final: 0.2255 (mp) REVERT: C 91 GLN cc_start: 0.8580 (pp30) cc_final: 0.8163 (pp30) outliers start: 31 outliers final: 28 residues processed: 186 average time/residue: 0.0961 time to fit residues: 25.8396 Evaluate side-chains 190 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 216 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 88 optimal weight: 0.0770 chunk 19 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 21 optimal weight: 0.0010 chunk 67 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 overall best weight: 0.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.203421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.145225 restraints weight = 12587.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.143104 restraints weight = 19840.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137967 restraints weight = 18085.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136770 restraints weight = 19691.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.137739 restraints weight = 16846.036| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10712 Z= 0.138 Angle : 0.614 11.903 14570 Z= 0.308 Chirality : 0.043 0.201 1694 Planarity : 0.004 0.055 1832 Dihedral : 4.260 24.565 1466 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.81 % Favored : 93.82 % Rotamer: Outliers : 2.80 % Allowed : 22.99 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.24), residues: 1342 helix: 1.01 (0.27), residues: 376 sheet: -0.46 (0.27), residues: 404 loop : -1.22 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 202 TYR 0.011 0.001 TYR C 142 PHE 0.026 0.002 PHE A 101 TRP 0.022 0.001 TRP A 33 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10692) covalent geometry : angle 0.61427 / 0.31 (14554) SS BOND : bond 0.00229 / 0.15 ( 8) SS BOND : angle 0.52544 / 0.31 ( 16) hydrogen bonds : bond 0.03264 / 2.20 ( 467) hydrogen bonds : angle 4.09490 / 3.00 ( 1296) metal coordination : bond 0.00161 / 0.14 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1950.66 seconds wall clock time: 34 minutes 33.17 seconds (2073.17 seconds total)