Starting phenix.real_space_refine on Sat Aug 23 07:17:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6j_28885/08_2025/8f6j_28885.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6j_28885/08_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_28885/08_2025/8f6j_28885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6j_28885/08_2025/8f6j_28885.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6j_28885/08_2025/8f6j_28885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6j_28885/08_2025/8f6j_28885.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 28 5.16 5 C 6676 2.51 5 N 1760 2.21 5 O 2000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10472 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2169 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1474 Classifications: {'peptide': 192} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "F" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1589 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "A" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2169 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain: "C" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1474 Classifications: {'peptide': 192} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "D" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1589 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.03, per 1000 atoms: 0.19 Number of scatterers: 10472 At special positions: 0 Unit cell: (67.977, 156.455, 145.665, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 28 16.00 O 2000 8.00 N 1760 7.00 C 6676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 213 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 313.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 250 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 234 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" ND1 HIS A 73 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 77 " pdb=" ZN A 304 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS A 263 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS B 285 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 250 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 234 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 77 " pdb="ZN ZN B 302 " - pdb=" ND1 HIS B 73 " pdb=" ZN B 304 " pdb="ZN ZN B 304 " - pdb=" NE2 HIS B 263 " pdb="ZN ZN B 304 " - pdb=" NE2 HIS A 285 " 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 24 sheets defined 33.1% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 12 through 34 removed outlier: 3.510A pdb=" N ARG B 16 " --> pdb=" O LYS B 12 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 41 through 67 removed outlier: 3.721A pdb=" N LEU B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 109 removed outlier: 4.484A pdb=" N ALA B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 142 removed outlier: 3.807A pdb=" N VAL B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 149 removed outlier: 3.632A pdb=" N VAL B 149 " --> pdb=" O SER B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 150 through 174 removed outlier: 3.791A pdb=" N HIS B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 178 through 208 removed outlier: 4.101A pdb=" N GLY B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 183 " --> pdb=" O TRP B 179 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN B 195 " --> pdb=" O TYR B 191 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 225 removed outlier: 3.595A pdb=" N LYS B 221 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.568A pdb=" N ILE B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 129 Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'F' and resid 90 through 94 removed outlier: 4.085A pdb=" N THR F 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing helix chain 'A' and resid 12 through 34 removed outlier: 3.522A pdb=" N THR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 67 removed outlier: 3.561A pdb=" N LEU A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 103 removed outlier: 4.470A pdb=" N ALA A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 95 " --> pdb=" O PHE A 91 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.958A pdb=" N ASN A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 141 removed outlier: 3.783A pdb=" N VAL A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 149 removed outlier: 3.564A pdb=" N VAL A 149 " --> pdb=" O SER A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 149' Processing helix chain 'A' and resid 150 through 175 removed outlier: 3.887A pdb=" N HIS A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 208 removed outlier: 4.220A pdb=" N ASP A 181 " --> pdb=" O TRP A 177 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 225 removed outlier: 3.593A pdb=" N LYS A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 removed outlier: 3.567A pdb=" N ILE A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.305A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 129 Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.517A pdb=" N GLU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 removed outlier: 4.076A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing sheet with id=AA1, first strand: chain 'B' and resid 233 through 240 removed outlier: 5.365A pdb=" N ASP B 235 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS B 250 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE B 249 " --> pdb=" O ILE B 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AA3, first strand: chain 'E' and resid 12 through 14 Processing sheet with id=AA4, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.807A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.053A pdb=" N ILE E 92 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR E 99 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER E 94 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 116 through 120 removed outlier: 3.644A pdb=" N SER E 116 " --> pdb=" O ASN E 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN E 139 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 134 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR E 175 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 178 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 6 through 10 removed outlier: 3.675A pdb=" N VAL F 8 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU F 21 " --> pdb=" O MET F 86 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU F 23 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 61 through 63 removed outlier: 5.649A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA F 52 " --> pdb=" O TRP F 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 106 through 107 Processing sheet with id=AB1, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.526A pdb=" N LEU F 158 " --> pdb=" O PHE F 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU F 141 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.526A pdb=" N LEU F 158 " --> pdb=" O PHE F 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU F 141 " --> pdb=" O GLY F 156 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP F 161 " --> pdb=" O TYR F 193 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 168 through 171 removed outlier: 3.694A pdb=" N THR F 168 " --> pdb=" O ASN F 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 233 through 240 removed outlier: 5.367A pdb=" N ASP A 235 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS A 250 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 249 " --> pdb=" O ILE A 283 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AB6, first strand: chain 'C' and resid 12 through 14 Processing sheet with id=AB7, first strand: chain 'C' and resid 46 through 49 removed outlier: 5.801A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.052A pdb=" N ILE C 92 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N THR C 99 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER C 94 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.661A pdb=" N SER C 116 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN C 139 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 134 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR C 175 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 178 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.519A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 21 " --> pdb=" O MET D 86 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 23 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 61 through 63 removed outlier: 5.645A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AC4, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.513A pdb=" N LEU D 158 " --> pdb=" O PHE D 139 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 141 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY D 156 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.513A pdb=" N LEU D 158 " --> pdb=" O PHE D 139 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 141 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY D 156 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 168 through 171 removed outlier: 3.683A pdb=" N THR D 168 " --> pdb=" O ASN D 216 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 1.04 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: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.750 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.320 ------------------------------------------------------------------------------- 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 : 6.52 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.04 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.24), residues: 1342 helix: 0.33 (0.27), residues: 366 sheet: -0.11 (0.29), residues: 370 loop : -0.78 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 202 TYR 0.008 0.001 TYR E 50 PHE 0.022 0.001 PHE A 49 TRP 0.008 0.001 TRP D 113 HIS 0.002 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00276 (10692) covalent geometry : angle 0.51361 (14554) SS BOND : bond 0.00111 ( 8) SS BOND : angle 0.46570 ( 16) hydrogen bonds : bond 0.28216 ( 467) hydrogen bonds : angle 8.66310 ( 1296) metal coordination : bond 0.00124 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.339 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: 0.0865 time to fit residues: 21.8163 Evaluate side-chains 155 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 ASN E 160 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.200289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.136080 restraints weight = 12497.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129654 restraints weight = 16631.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122737 restraints weight = 12751.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122687 restraints weight = 14484.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122879 restraints weight = 12732.851| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 10712 Z= 0.299 Angle : 0.694 9.316 14570 Z= 0.369 Chirality : 0.048 0.174 1694 Planarity : 0.006 0.078 1832 Dihedral : 4.646 25.262 1466 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.75 % Favored : 91.88 % Rotamer: Outliers : 1.31 % Allowed : 13.29 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.24), residues: 1342 helix: 0.31 (0.25), residues: 390 sheet: -0.47 (0.28), residues: 400 loop : -1.20 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 202 TYR 0.019 0.002 TYR D 162 PHE 0.017 0.002 PHE B 49 TRP 0.017 0.002 TRP F 50 HIS 0.006 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00696 (10692) covalent geometry : angle 0.69461 (14554) SS BOND : bond 0.00433 ( 8) SS BOND : angle 0.45758 ( 16) hydrogen bonds : bond 0.05834 ( 467) hydrogen bonds : angle 5.45838 ( 1296) metal coordination : bond 0.00454 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.306 Fit side-chains REVERT: B 101 PHE cc_start: 0.8106 (t80) cc_final: 0.7897 (t80) REVERT: F 193 TYR cc_start: 0.8475 (m-80) cc_final: 0.8180 (m-10) REVERT: F 226 LYS cc_start: 0.8123 (tppp) cc_final: 0.7705 (tptp) REVERT: A 101 PHE cc_start: 0.8262 (t80) cc_final: 0.8009 (t80) REVERT: D 193 TYR cc_start: 0.8453 (m-80) cc_final: 0.8173 (m-10) REVERT: D 226 LYS cc_start: 0.8178 (tppp) cc_final: 0.7782 (tptp) outliers start: 15 outliers final: 12 residues processed: 174 average time/residue: 0.0948 time to fit residues: 23.5063 Evaluate side-chains 159 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 216 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 122 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 133 optimal weight: 0.0070 chunk 102 optimal weight: 0.6980 chunk 69 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.204672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.162483 restraints weight = 12694.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.147367 restraints weight = 16519.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143800 restraints weight = 22448.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.143546 restraints weight = 22455.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143878 restraints weight = 18742.939| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10712 Z= 0.171 Angle : 0.589 9.323 14570 Z= 0.309 Chirality : 0.043 0.143 1694 Planarity : 0.004 0.065 1832 Dihedral : 4.439 25.386 1466 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.59 % Favored : 94.11 % Rotamer: Outliers : 2.01 % Allowed : 15.91 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.24), residues: 1342 helix: 0.59 (0.26), residues: 378 sheet: -0.47 (0.28), residues: 400 loop : -1.19 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 202 TYR 0.020 0.001 TYR C 142 PHE 0.019 0.002 PHE B 49 TRP 0.011 0.001 TRP F 39 HIS 0.004 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00391 (10692) covalent geometry : angle 0.58914 (14554) SS BOND : bond 0.00314 ( 8) SS BOND : angle 0.50586 ( 16) hydrogen bonds : bond 0.04682 ( 467) hydrogen bonds : angle 4.90132 ( 1296) metal coordination : bond 0.00228 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.270 Fit side-chains REVERT: E 91 GLN cc_start: 0.8960 (pp30) cc_final: 0.8626 (pp30) REVERT: A 101 PHE cc_start: 0.7159 (t80) cc_final: 0.6746 (t80) REVERT: A 205 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7536 (mm-40) REVERT: C 91 GLN cc_start: 0.8895 (pp30) cc_final: 0.8488 (pp30) REVERT: C 169 ASP cc_start: 0.8024 (m-30) cc_final: 0.7673 (m-30) outliers start: 23 outliers final: 17 residues processed: 184 average time/residue: 0.0950 time to fit residues: 24.5110 Evaluate side-chains 175 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 191 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 216 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.8834 > 50: distance: 36 - 42: 16.662 distance: 42 - 43: 25.758 distance: 43 - 44: 26.452 distance: 43 - 46: 41.683 distance: 44 - 45: 60.712 distance: 44 - 50: 21.676 distance: 46 - 47: 22.745 distance: 46 - 48: 18.923 distance: 47 - 49: 6.120 distance: 50 - 51: 17.401 distance: 51 - 52: 21.491 distance: 51 - 54: 22.617 distance: 52 - 53: 5.302 distance: 52 - 59: 35.404 distance: 54 - 55: 19.244 distance: 55 - 56: 16.258 distance: 56 - 57: 11.671 distance: 57 - 58: 9.405 distance: 59 - 60: 27.633 distance: 60 - 61: 4.902 distance: 61 - 62: 35.845 distance: 61 - 63: 36.345 distance: 63 - 64: 18.306 distance: 63 - 69: 34.890 distance: 64 - 65: 23.244 distance: 64 - 67: 8.914 distance: 65 - 66: 11.883 distance: 65 - 70: 24.924 distance: 67 - 68: 11.127 distance: 68 - 69: 19.517 distance: 70 - 71: 5.706 distance: 70 - 150: 12.586 distance: 71 - 72: 11.631 distance: 72 - 73: 7.668 distance: 72 - 76: 11.067 distance: 73 - 147: 19.563 distance: 74 - 75: 18.315 distance: 76 - 77: 23.551 distance: 77 - 78: 44.871 distance: 77 - 80: 20.937 distance: 78 - 79: 43.360 distance: 78 - 83: 16.942 distance: 80 - 81: 25.734 distance: 80 - 82: 31.365 distance: 83 - 84: 12.008 distance: 83 - 138: 19.205 distance: 84 - 85: 35.700 distance: 84 - 87: 24.925 distance: 85 - 86: 41.821 distance: 85 - 94: 45.698 distance: 87 - 88: 18.931 distance: 88 - 89: 7.800 distance: 88 - 90: 13.357 distance: 89 - 91: 10.936 distance: 90 - 92: 11.913 distance: 91 - 93: 5.834 distance: 92 - 93: 12.980 distance: 94 - 95: 21.761 distance: 94 - 100: 38.429 distance: 95 - 96: 36.165 distance: 95 - 98: 18.552 distance: 96 - 97: 21.923 distance: 96 - 101: 25.508 distance: 98 - 99: 29.587 distance: 99 - 100: 25.953 distance: 101 - 102: 8.055 distance: 102 - 103: 20.941 distance: 102 - 105: 30.042 distance: 103 - 104: 17.286 distance: 103 - 109: 14.210 distance: 105 - 106: 23.039 distance: 106 - 107: 11.140 distance: 106 - 108: 17.291 distance: 109 - 110: 10.538 distance: 110 - 111: 36.935 distance: 110 - 113: 33.643 distance: 111 - 112: 30.851 distance: 111 - 114: 19.604