Starting phenix.real_space_refine on Mon Jun 9 10:33:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6j_28885/06_2025/8f6j_28885.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6j_28885/06_2025/8f6j_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8f6j_28885/06_2025/8f6j_28885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6j_28885/06_2025/8f6j_28885.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6j_28885/06_2025/8f6j_28885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6j_28885/06_2025/8f6j_28885.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.55, per 1000 atoms: 0.63 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: 3.03 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" 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: 1.17 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: 2.70 Time building geometry restraints manager: 2.79 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: 1.530 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.450 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 : 6.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (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 TRP 0.008 0.001 TRP D 113 HIS 0.002 0.001 HIS A 155 PHE 0.022 0.001 PHE A 49 TYR 0.008 0.001 TYR E 50 ARG 0.004 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.28216 ( 467) hydrogen bonds : angle 8.66310 ( 1296) metal coordination : bond 0.00124 ( 12) SS BOND : bond 0.00111 ( 8) SS BOND : angle 0.46570 ( 16) covalent geometry : bond 0.00276 (10692) covalent geometry : angle 0.51361 (14554) *********************** 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 : 1.208 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: 0.2281 time to fit residues: 56.8643 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 : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.0980 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 40 optimal weight: 0.0040 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN E 160 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4376 r_free = 0.4376 target = 0.206911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.157311 restraints weight = 12593.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.151963 restraints weight = 21541.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.148703 restraints weight = 20434.586| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10712 Z= 0.153 Angle : 0.601 9.499 14570 Z= 0.315 Chirality : 0.044 0.169 1694 Planarity : 0.005 0.073 1832 Dihedral : 4.204 26.007 1466 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.48 % Favored : 93.14 % Rotamer: Outliers : 0.79 % Allowed : 12.24 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.24), residues: 1342 helix: 0.40 (0.25), residues: 390 sheet: -0.22 (0.28), residues: 410 loop : -1.09 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 33 HIS 0.003 0.001 HIS A 155 PHE 0.017 0.001 PHE B 49 TYR 0.019 0.002 TYR D 162 ARG 0.004 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.05759 ( 467) hydrogen bonds : angle 5.44538 ( 1296) metal coordination : bond 0.00155 ( 12) SS BOND : bond 0.00445 ( 8) SS BOND : angle 0.68058 ( 16) covalent geometry : bond 0.00328 (10692) covalent geometry : angle 0.60079 (14554) *********************** 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 178 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 1.147 Fit side-chains REVERT: F 162 TYR cc_start: 0.7709 (p90) cc_final: 0.7473 (p90) REVERT: C 91 GLN cc_start: 0.8806 (pp30) cc_final: 0.8353 (pp30) outliers start: 9 outliers final: 6 residues processed: 174 average time/residue: 0.2246 time to fit residues: 55.3549 Evaluate side-chains 158 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 HIS 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 D residue 10 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 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 95 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS 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 = 0.4360 r_free = 0.4360 target = 0.205417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148779 restraints weight = 12698.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.147786 restraints weight = 21606.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147157 restraints weight = 21080.531| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10712 Z= 0.174 Angle : 0.585 9.522 14570 Z= 0.307 Chirality : 0.043 0.146 1694 Planarity : 0.004 0.063 1832 Dihedral : 4.303 26.024 1466 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.33 % Favored : 93.37 % Rotamer: Outliers : 2.01 % Allowed : 15.12 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.24), residues: 1342 helix: 0.55 (0.26), residues: 390 sheet: -0.38 (0.27), residues: 402 loop : -1.07 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 113 HIS 0.003 0.001 HIS B 155 PHE 0.020 0.002 PHE A 101 TYR 0.019 0.001 TYR C 142 ARG 0.002 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 467) hydrogen bonds : angle 4.84861 ( 1296) metal coordination : bond 0.00265 ( 12) SS BOND : bond 0.00331 ( 8) SS BOND : angle 0.53402 ( 16) covalent geometry : bond 0.00398 (10692) covalent geometry : angle 0.58491 (14554) *********************** 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 : 1.253 Fit side-chains revert: symmetry clash REVERT: E 91 GLN cc_start: 0.8744 (pp30) cc_final: 0.8277 (pp30) REVERT: F 162 TYR cc_start: 0.7731 (p90) cc_final: 0.7479 (p90) REVERT: F 226 LYS cc_start: 0.8426 (tptp) cc_final: 0.8162 (tptp) REVERT: A 205 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7527 (mm-40) REVERT: C 91 GLN cc_start: 0.8767 (pp30) cc_final: 0.8273 (pp30) REVERT: C 169 ASP cc_start: 0.8036 (m-30) cc_final: 0.7715 (m-30) REVERT: D 226 LYS cc_start: 0.8402 (tptp) cc_final: 0.8200 (tptp) outliers start: 23 outliers final: 14 residues processed: 181 average time/residue: 0.2327 time to fit residues: 58.8149 Evaluate side-chains 171 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 74 SER 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 A residue 205 GLN Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain C residue 66 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 197 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 51 optimal weight: 0.3980 chunk 41 optimal weight: 7.9990 chunk 13 optimal weight: 0.0870 chunk 104 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 123 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4376 r_free = 0.4376 target = 0.207098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.148455 restraints weight = 12536.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137432 restraints weight = 16357.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133395 restraints weight = 12394.703| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10712 Z= 0.120 Angle : 0.554 9.945 14570 Z= 0.289 Chirality : 0.042 0.218 1694 Planarity : 0.004 0.058 1832 Dihedral : 4.163 25.811 1466 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.77 % Favored : 94.93 % Rotamer: Outliers : 2.36 % Allowed : 17.74 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1342 helix: 0.62 (0.26), residues: 392 sheet: -0.26 (0.28), residues: 388 loop : -1.10 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 113 HIS 0.003 0.001 HIS B 155 PHE 0.024 0.002 PHE A 49 TYR 0.021 0.001 TYR E 142 ARG 0.008 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 467) hydrogen bonds : angle 4.53663 ( 1296) metal coordination : bond 0.00085 ( 12) SS BOND : bond 0.00294 ( 8) SS BOND : angle 0.44934 ( 16) covalent geometry : bond 0.00262 (10692) covalent geometry : angle 0.55430 (14554) *********************** 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 193 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.085 Fit side-chains REVERT: E 91 GLN cc_start: 0.8800 (pp30) cc_final: 0.8370 (pp30) REVERT: E 169 ASP cc_start: 0.8489 (m-30) cc_final: 0.7893 (m-30) REVERT: F 162 TYR cc_start: 0.7950 (p90) cc_final: 0.7712 (p90) REVERT: F 226 LYS cc_start: 0.7873 (tptp) cc_final: 0.7588 (tppp) REVERT: A 33 TRP cc_start: 0.5712 (t60) cc_final: 0.5496 (t60) REVERT: C 91 GLN cc_start: 0.8917 (pp30) cc_final: 0.8588 (pp30) REVERT: C 169 ASP cc_start: 0.8465 (m-30) cc_final: 0.7916 (m-30) REVERT: C 174 THR cc_start: 0.9012 (t) cc_final: 0.8632 (t) outliers start: 27 outliers final: 13 residues processed: 185 average time/residue: 0.2153 time to fit residues: 56.5539 Evaluate side-chains 171 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 66 SER 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 A residue 99 LEU Chi-restraints excluded: chain C residue 66 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 81 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 114 optimal weight: 0.0570 chunk 113 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 248 GLN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.206399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143672 restraints weight = 12504.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 85)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.133591 restraints weight = 19487.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.131441 restraints weight = 12875.272| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2167 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= 0.136 Angle : 0.583 12.548 14570 Z= 0.298 Chirality : 0.042 0.210 1694 Planarity : 0.004 0.055 1832 Dihedral : 4.164 25.661 1466 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.96 % Favored : 93.67 % Rotamer: Outliers : 2.27 % Allowed : 19.58 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1342 helix: 0.66 (0.26), residues: 392 sheet: -0.36 (0.26), residues: 414 loop : -1.08 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 33 HIS 0.003 0.001 HIS B 155 PHE 0.020 0.001 PHE A 97 TYR 0.021 0.001 TYR C 142 ARG 0.008 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 467) hydrogen bonds : angle 4.35387 ( 1296) metal coordination : bond 0.00161 ( 12) SS BOND : bond 0.00285 ( 8) SS BOND : angle 0.43662 ( 16) covalent geometry : bond 0.00307 (10692) covalent geometry : angle 0.58286 (14554) *********************** 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 188 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: B 191 TYR cc_start: 0.7381 (t80) cc_final: 0.7077 (t80) REVERT: B 205 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7577 (tp40) REVERT: E 91 GLN cc_start: 0.8800 (pp30) cc_final: 0.8478 (pp30) REVERT: E 169 ASP cc_start: 0.8425 (m-30) cc_final: 0.8123 (m-30) REVERT: A 33 TRP cc_start: 0.5712 (t60) cc_final: 0.5507 (t60) REVERT: C 91 GLN cc_start: 0.8910 (pp30) cc_final: 0.8632 (pp30) REVERT: C 169 ASP cc_start: 0.8354 (m-30) cc_final: 0.8058 (m-30) REVERT: C 174 THR cc_start: 0.9051 (t) cc_final: 0.8736 (t) outliers start: 26 outliers final: 18 residues processed: 182 average time/residue: 0.2243 time to fit residues: 57.5327 Evaluate side-chains 176 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 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 F residue 197 SER 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 C residue 66 SER 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 87 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 46 optimal weight: 0.4980 chunk 123 optimal weight: 0.9990 chunk 130 optimal weight: 0.0040 chunk 12 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 48 optimal weight: 0.3980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN ** E 200 HIS ** 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 = 0.4381 r_free = 0.4381 target = 0.207472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.134111 restraints weight = 12552.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131112 restraints weight = 13413.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131725 restraints weight = 12192.416| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10712 Z= 0.116 Angle : 0.572 11.195 14570 Z= 0.289 Chirality : 0.042 0.199 1694 Planarity : 0.004 0.053 1832 Dihedral : 4.085 25.214 1466 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.14 % Favored : 94.49 % Rotamer: Outliers : 2.45 % Allowed : 20.28 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1342 helix: 0.72 (0.26), residues: 392 sheet: -0.20 (0.27), residues: 406 loop : -1.14 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 33 HIS 0.003 0.001 HIS B 155 PHE 0.028 0.002 PHE A 49 TYR 0.022 0.001 TYR E 142 ARG 0.005 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 467) hydrogen bonds : angle 4.20920 ( 1296) metal coordination : bond 0.00097 ( 12) SS BOND : bond 0.00249 ( 8) SS BOND : angle 0.42122 ( 16) covalent geometry : bond 0.00260 (10692) covalent geometry : angle 0.57246 (14554) *********************** 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 189 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: B 191 TYR cc_start: 0.7263 (t80) cc_final: 0.7015 (t80) REVERT: E 91 GLN cc_start: 0.8873 (pp30) cc_final: 0.8662 (pp30) REVERT: E 169 ASP cc_start: 0.8345 (m-30) cc_final: 0.8068 (m-30) REVERT: A 23 LEU cc_start: 0.8403 (tp) cc_final: 0.8132 (tt) REVERT: C 91 GLN cc_start: 0.8824 (pp30) cc_final: 0.8521 (pp30) REVERT: C 163 GLU cc_start: 0.8288 (pm20) cc_final: 0.8079 (pm20) REVERT: C 169 ASP cc_start: 0.8324 (m-30) cc_final: 0.8051 (m-30) REVERT: C 174 THR cc_start: 0.9010 (t) cc_final: 0.8690 (t) REVERT: D 226 LYS cc_start: 0.8200 (tppp) cc_final: 0.7691 (tptp) outliers start: 28 outliers final: 18 residues processed: 182 average time/residue: 0.3028 time to fit residues: 78.6127 Evaluate side-chains 174 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain E residue 66 SER 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 F residue 159 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 197 SER 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 C residue 66 SER 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 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 59 optimal weight: 0.0470 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN D 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.206115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.144678 restraints weight = 12726.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.141779 restraints weight = 19364.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136023 restraints weight = 15875.256| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10712 Z= 0.145 Angle : 0.596 12.715 14570 Z= 0.302 Chirality : 0.042 0.188 1694 Planarity : 0.004 0.052 1832 Dihedral : 4.127 24.869 1466 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.41 % Favored : 93.22 % Rotamer: Outliers : 2.71 % Allowed : 21.33 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.24), residues: 1342 helix: 1.00 (0.27), residues: 376 sheet: -0.30 (0.27), residues: 416 loop : -1.16 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 33 HIS 0.004 0.001 HIS B 155 PHE 0.029 0.001 PHE A 101 TYR 0.020 0.001 TYR E 142 ARG 0.010 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 467) hydrogen bonds : angle 4.19313 ( 1296) metal coordination : bond 0.00199 ( 12) SS BOND : bond 0.00255 ( 8) SS BOND : angle 0.45772 ( 16) covalent geometry : bond 0.00333 (10692) covalent geometry : angle 0.59619 (14554) *********************** 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 196 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: E 91 GLN cc_start: 0.8771 (pp30) cc_final: 0.8460 (pp30) REVERT: E 163 GLU cc_start: 0.8095 (pm20) cc_final: 0.7879 (pm20) REVERT: E 174 THR cc_start: 0.9008 (t) cc_final: 0.8681 (t) REVERT: F 226 LYS cc_start: 0.8252 (tppp) cc_final: 0.7854 (tmtt) REVERT: A 23 LEU cc_start: 0.8109 (tp) cc_final: 0.7897 (tt) REVERT: A 101 PHE cc_start: 0.7565 (t80) cc_final: 0.7361 (t80) REVERT: A 141 LEU cc_start: 0.1981 (OUTLIER) cc_final: 0.1648 (mp) REVERT: C 91 GLN cc_start: 0.8855 (pp30) cc_final: 0.8614 (pp30) REVERT: C 174 THR cc_start: 0.8983 (t) cc_final: 0.8626 (t) REVERT: D 226 LYS cc_start: 0.8393 (tppp) cc_final: 0.8030 (tptp) outliers start: 31 outliers final: 23 residues processed: 189 average time/residue: 0.2850 time to fit residues: 76.9859 Evaluate side-chains 186 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 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 169 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 216 ASN 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 C residue 66 SER 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 138 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 9 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 0.0670 chunk 21 optimal weight: 0.0770 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 chunk 117 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 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 = 0.4376 r_free = 0.4376 target = 0.206962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145437 restraints weight = 12549.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143209 restraints weight = 17426.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137900 restraints weight = 14435.990| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 0.031 10712 Z= 0.121 Angle : 0.583 12.114 14570 Z= 0.293 Chirality : 0.042 0.193 1694 Planarity : 0.004 0.051 1832 Dihedral : 4.093 24.404 1466 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.07 % Favored : 94.56 % Rotamer: Outliers : 2.53 % Allowed : 21.50 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1342 helix: 1.04 (0.27), residues: 376 sheet: -0.26 (0.27), residues: 416 loop : -1.14 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 33 HIS 0.003 0.001 HIS B 155 PHE 0.031 0.002 PHE A 101 TYR 0.019 0.001 TYR E 142 ARG 0.012 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 467) hydrogen bonds : angle 4.13213 ( 1296) metal coordination : bond 0.00116 ( 12) SS BOND : bond 0.00432 ( 8) SS BOND : angle 0.79625 ( 16) covalent geometry : bond 0.00274 (10692) covalent geometry : angle 0.58320 (14554) *********************** 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 194 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: E 91 GLN cc_start: 0.8752 (pp30) cc_final: 0.8517 (pp30) REVERT: A 23 LEU cc_start: 0.8103 (tp) cc_final: 0.7888 (tt) REVERT: A 141 LEU cc_start: 0.2136 (OUTLIER) cc_final: 0.1729 (mp) REVERT: C 91 GLN cc_start: 0.8906 (pp30) cc_final: 0.8537 (pp30) REVERT: C 163 GLU cc_start: 0.8006 (pm20) cc_final: 0.7796 (pm20) REVERT: C 174 THR cc_start: 0.8889 (t) cc_final: 0.8682 (t) outliers start: 29 outliers final: 26 residues processed: 186 average time/residue: 0.2203 time to fit residues: 58.1276 Evaluate side-chains 186 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain E residue 38 GLN 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 159 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 66 SER 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 138 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 216 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 92 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 20 optimal weight: 0.0030 chunk 40 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 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 = 0.4360 r_free = 0.4360 target = 0.205172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3717 r_free = 0.3717 target = 0.142182 restraints weight = 12692.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132394 restraints weight = 16777.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131114 restraints weight = 13831.124| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10712 Z= 0.160 Angle : 0.617 11.790 14570 Z= 0.309 Chirality : 0.043 0.195 1694 Planarity : 0.004 0.053 1832 Dihedral : 4.199 24.219 1466 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.93 % Favored : 92.70 % Rotamer: Outliers : 2.53 % Allowed : 22.20 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1342 helix: 1.05 (0.27), residues: 376 sheet: -0.35 (0.27), residues: 404 loop : -1.19 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 33 HIS 0.003 0.001 HIS A 285 PHE 0.025 0.001 PHE A 97 TYR 0.022 0.001 TYR C 142 ARG 0.010 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 467) hydrogen bonds : angle 4.17647 ( 1296) metal coordination : bond 0.00245 ( 12) SS BOND : bond 0.00611 ( 8) SS BOND : angle 1.28035 ( 16) covalent geometry : bond 0.00372 (10692) covalent geometry : angle 0.61614 (14554) *********************** 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 189 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: B 207 LEU cc_start: 0.7659 (tt) cc_final: 0.7139 (tt) REVERT: E 91 GLN cc_start: 0.8917 (pp30) cc_final: 0.8514 (pp30) REVERT: A 141 LEU cc_start: 0.2236 (OUTLIER) cc_final: 0.1840 (mp) REVERT: C 91 GLN cc_start: 0.8868 (pp30) cc_final: 0.8469 (pp30) REVERT: C 163 GLU cc_start: 0.8087 (pm20) cc_final: 0.7786 (pm20) REVERT: D 92 GLU cc_start: 0.7727 (tp30) cc_final: 0.7519 (tp30) outliers start: 29 outliers final: 26 residues processed: 182 average time/residue: 0.2244 time to fit residues: 58.3073 Evaluate side-chains 183 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 195 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 169 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 66 SER 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 159 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 197 SER 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 92 optimal weight: 0.7980 chunk 104 optimal weight: 0.0770 chunk 106 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 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 = 0.4367 r_free = 0.4367 target = 0.206032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145400 restraints weight = 12605.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.143255 restraints weight = 17933.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137914 restraints weight = 14499.044| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10712 Z= 0.139 Angle : 0.617 12.095 14570 Z= 0.308 Chirality : 0.042 0.190 1694 Planarity : 0.004 0.054 1832 Dihedral : 4.191 23.966 1466 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.29 % Favored : 94.34 % Rotamer: Outliers : 2.62 % Allowed : 22.29 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.24), residues: 1342 helix: 0.98 (0.27), residues: 376 sheet: -0.35 (0.27), residues: 404 loop : -1.17 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 33 HIS 0.003 0.001 HIS B 155 PHE 0.024 0.002 PHE A 97 TYR 0.023 0.001 TYR C 142 ARG 0.009 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.03256 ( 467) hydrogen bonds : angle 4.14271 ( 1296) metal coordination : bond 0.00176 ( 12) SS BOND : bond 0.00416 ( 8) SS BOND : angle 1.16993 ( 16) covalent geometry : bond 0.00321 (10692) covalent geometry : angle 0.61623 (14554) ********************** 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 192 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: B 161 PHE cc_start: 0.7182 (m-80) cc_final: 0.6901 (m-80) REVERT: E 91 GLN cc_start: 0.8757 (pp30) cc_final: 0.8491 (pp30) REVERT: A 141 LEU cc_start: 0.2453 (OUTLIER) cc_final: 0.2052 (mp) REVERT: C 91 GLN cc_start: 0.8865 (pp30) cc_final: 0.8454 (pp30) outliers start: 30 outliers final: 26 residues processed: 185 average time/residue: 0.2216 time to fit residues: 58.2663 Evaluate side-chains 187 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 195 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 169 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 216 ASN 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 C residue 38 GLN Chi-restraints excluded: chain C residue 66 SER 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 138 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 197 SER 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 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 133 optimal weight: 0.0670 chunk 94 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 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 = 0.4367 r_free = 0.4367 target = 0.206083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145553 restraints weight = 12504.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143078 restraints weight = 17696.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.143238 restraints weight = 17524.762| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2747 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= 0.134 Angle : 0.618 12.570 14570 Z= 0.307 Chirality : 0.043 0.297 1694 Planarity : 0.004 0.054 1832 Dihedral : 4.149 23.958 1466 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.26 % Favored : 93.37 % Rotamer: Outliers : 2.53 % Allowed : 23.16 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.24), residues: 1342 helix: 1.05 (0.27), residues: 376 sheet: -0.35 (0.27), residues: 404 loop : -1.16 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 33 HIS 0.003 0.001 HIS B 155 PHE 0.023 0.001 PHE A 97 TYR 0.023 0.001 TYR C 142 ARG 0.008 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 467) hydrogen bonds : angle 4.12226 ( 1296) metal coordination : bond 0.00159 ( 12) SS BOND : bond 0.00440 ( 8) SS BOND : angle 1.05480 ( 16) covalent geometry : bond 0.00308 (10692) covalent geometry : angle 0.61774 (14554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4312.53 seconds wall clock time: 77 minutes 37.13 seconds (4657.13 seconds total)