Starting phenix.real_space_refine on Fri Jul 3 13:52:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcr_37447/07_2026/8wcr_37447.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcr_37447/07_2026/8wcr_37447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wcr_37447/07_2026/8wcr_37447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcr_37447/07_2026/8wcr_37447.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wcr_37447/07_2026/8wcr_37447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcr_37447/07_2026/8wcr_37447.map" } resolution = 2.74 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= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 40 5.49 5 S 20 5.16 5 Cl 5 4.86 5 C 9620 2.51 5 N 2070 2.21 5 O 2860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14615 Number of models: 1 Model: "" Number of chains: 15 Chain: "E" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "A" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "B" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "C" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "D" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "E" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 331 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 1 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 331 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 9} Classifications: {'undetermined': 9} Link IDs: {None: 7} Chain breaks: 1 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 331 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 9} Classifications: {'undetermined': 9} Link IDs: {None: 7} Chain breaks: 1 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 331 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 9} Classifications: {'undetermined': 9} Link IDs: {None: 7} Chain breaks: 1 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 331 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 9} Classifications: {'undetermined': 9} Link IDs: {None: 7} Chain breaks: 1 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Time building chain proxies: 4.86, per 1000 atoms: 0.33 Number of scatterers: 14615 At special positions: 0 Unit cell: (91.2, 92.72, 128.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 5 17.00 S 20 16.00 P 40 15.00 O 2860 8.00 N 2070 7.00 C 9620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.97 Conformation dependent library (CDL) restraints added in 897.9 milliseconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 41.3% alpha, 45.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'E' and resid 50 through 53 Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 146 through 149 removed outlier: 3.907A pdb=" N VAL E 149 " --> pdb=" O LEU E 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 146 through 149' Processing helix chain 'E' and resid 196 through 213 removed outlier: 5.265A pdb=" N LEU E 203 " --> pdb=" O PRO E 199 " (cutoff:3.500A) Proline residue: E 204 - end of helix Processing helix chain 'E' and resid 214 through 218 removed outlier: 3.651A pdb=" N SER E 218 " --> pdb=" O ALA E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 244 Processing helix chain 'E' and resid 253 through 282 Processing helix chain 'E' and resid 284 through 316 removed outlier: 3.553A pdb=" N ALA E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing helix chain 'A' and resid 50 through 53 Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 146 through 149 removed outlier: 3.907A pdb=" N VAL A 149 " --> pdb=" O LEU A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 149' Processing helix chain 'A' and resid 196 through 213 removed outlier: 5.266A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.652A pdb=" N SER A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 244 Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 316 removed outlier: 3.553A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 50 through 53 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 146 through 149 removed outlier: 3.907A pdb=" N VAL B 149 " --> pdb=" O LEU B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 196 through 213 removed outlier: 5.266A pdb=" N LEU B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 214 through 218 removed outlier: 3.651A pdb=" N SER B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 244 Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 284 through 316 removed outlier: 3.553A pdb=" N ALA B 288 " --> pdb=" O GLN B 284 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'C' and resid 50 through 53 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 146 through 149 removed outlier: 3.908A pdb=" N VAL C 149 " --> pdb=" O LEU C 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 146 through 149' Processing helix chain 'C' and resid 196 through 213 removed outlier: 5.266A pdb=" N LEU C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Proline residue: C 204 - end of helix Processing helix chain 'C' and resid 214 through 218 removed outlier: 3.651A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 244 Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 284 through 316 removed outlier: 3.553A pdb=" N ALA C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 50 through 53 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 146 through 149 removed outlier: 3.908A pdb=" N VAL D 149 " --> pdb=" O LEU D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 196 through 213 removed outlier: 5.266A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Proline residue: D 204 - end of helix Processing helix chain 'D' and resid 214 through 218 removed outlier: 3.651A pdb=" N SER D 218 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 244 Processing helix chain 'D' and resid 253 through 282 Processing helix chain 'D' and resid 284 through 316 removed outlier: 3.554A pdb=" N ALA D 288 " --> pdb=" O GLN D 284 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing sheet with id=AA1, first strand: chain 'E' and resid 64 through 65 removed outlier: 5.670A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR E 36 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU E 30 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE E 42 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU E 24 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER E 44 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE E 22 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER E 46 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR E 20 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS E 48 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL E 18 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 64 through 65 removed outlier: 5.670A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR E 36 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU E 30 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE E 42 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU E 24 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER E 44 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE E 22 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER E 46 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR E 20 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS E 48 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL E 18 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 76 through 78 removed outlier: 11.076A pdb=" N ARG E 179 " --> pdb=" O ASN E 173 " (cutoff:3.500A) removed outlier: 9.811A pdb=" N ASN E 173 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N GLU E 181 " --> pdb=" O PRO E 171 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N LYS E 183 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL E 169 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 64 through 65 removed outlier: 5.671A pdb=" N ALA A 87 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER A 107 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR A 36 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 30 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU A 24 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER A 44 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE A 22 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER A 46 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR A 20 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS A 48 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL A 18 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A 16 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ALA A 143 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL A 18 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 64 through 65 removed outlier: 5.671A pdb=" N ALA A 87 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER A 107 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR A 36 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 30 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU A 24 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER A 44 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE A 22 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER A 46 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR A 20 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS A 48 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL A 18 " --> pdb=" O LYS A 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 76 through 78 removed outlier: 11.077A pdb=" N ARG A 179 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 9.812A pdb=" N ASN A 173 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N GLU A 181 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N LYS A 183 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL A 169 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 65 removed outlier: 5.670A pdb=" N ALA B 87 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER B 107 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR B 36 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 30 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE B 42 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU B 24 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER B 44 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE B 22 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER B 46 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR B 20 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS B 48 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N VAL B 18 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA B 143 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 65 removed outlier: 5.670A pdb=" N ALA B 87 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER B 107 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR B 36 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 30 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE B 42 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU B 24 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER B 44 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE B 22 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER B 46 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR B 20 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS B 48 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N VAL B 18 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 76 through 78 removed outlier: 11.077A pdb=" N ARG B 179 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 9.811A pdb=" N ASN B 173 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N GLU B 181 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N LYS B 183 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL B 169 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 64 through 65 removed outlier: 5.671A pdb=" N ALA C 87 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER C 107 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR C 36 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU C 30 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE C 42 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU C 24 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER C 44 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE C 22 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER C 46 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR C 20 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS C 48 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL C 18 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 64 through 65 removed outlier: 5.671A pdb=" N ALA C 87 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER C 107 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR C 36 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU C 30 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE C 42 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU C 24 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER C 44 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE C 22 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER C 46 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N THR C 20 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N LYS C 48 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL C 18 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 removed outlier: 11.077A pdb=" N ARG C 179 " --> pdb=" O ASN C 173 " (cutoff:3.500A) removed outlier: 9.812A pdb=" N ASN C 173 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N GLU C 181 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N LYS C 183 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N VAL C 169 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 64 through 65 removed outlier: 5.670A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR D 36 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU D 30 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE D 42 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU D 24 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N SER D 44 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE D 22 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER D 46 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR D 20 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N LYS D 48 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL D 18 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA D 143 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL D 18 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 64 through 65 removed outlier: 5.670A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR D 36 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU D 30 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE D 42 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU D 24 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N SER D 44 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE D 22 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER D 46 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR D 20 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N LYS D 48 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL D 18 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 11.077A pdb=" N ARG D 179 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 9.811A pdb=" N ASN D 173 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N GLU D 181 " --> pdb=" O PRO D 171 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N LYS D 183 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL D 169 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) 725 hydrogen bonds defined for protein. 2080 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: 1.60 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2083 1.32 - 1.44: 3889 1.44 - 1.56: 8551 1.56 - 1.69: 82 1.69 - 1.81: 35 Bond restraints: 14640 Sorted by residual: bond pdb=" CB AARG B 293 " pdb=" CG AARG B 293 " ideal model delta sigma weight residual 1.520 1.635 -0.115 3.00e-02 1.11e+03 1.47e+01 bond pdb=" CB BARG B 293 " pdb=" CG BARG B 293 " ideal model delta sigma weight residual 1.520 1.609 -0.089 3.00e-02 1.11e+03 8.82e+00 bond pdb=" CE1 TYR D 251 " pdb=" CZ TYR D 251 " ideal model delta sigma weight residual 1.378 1.432 -0.054 2.40e-02 1.74e+03 5.03e+00 bond pdb=" CE1 TYR E 251 " pdb=" CZ TYR E 251 " ideal model delta sigma weight residual 1.378 1.432 -0.054 2.40e-02 1.74e+03 4.99e+00 bond pdb=" CE1 TYR C 251 " pdb=" CZ TYR C 251 " ideal model delta sigma weight residual 1.378 1.432 -0.054 2.40e-02 1.74e+03 4.98e+00 ... (remaining 14635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 19247 2.58 - 5.16: 349 5.16 - 7.75: 23 7.75 - 10.33: 0 10.33 - 12.91: 1 Bond angle restraints: 19620 Sorted by residual: angle pdb=" CB AARG B 293 " pdb=" CG AARG B 293 " pdb=" CD AARG B 293 " ideal model delta sigma weight residual 111.30 98.39 12.91 2.30e+00 1.89e-01 3.15e+01 angle pdb=" CD AARG B 293 " pdb=" NE AARG B 293 " pdb=" CZ AARG B 293 " ideal model delta sigma weight residual 124.40 117.71 6.69 1.40e+00 5.10e-01 2.28e+01 angle pdb=" C ARG B 293 " pdb=" CA BARG B 293 " pdb=" CB BARG B 293 " ideal model delta sigma weight residual 110.79 105.20 5.59 1.66e+00 3.63e-01 1.13e+01 angle pdb=" CA BARG B 293 " pdb=" CB BARG B 293 " pdb=" CG BARG B 293 " ideal model delta sigma weight residual 114.10 108.20 5.90 2.00e+00 2.50e-01 8.71e+00 angle pdb=" CB GLU C 163 " pdb=" CG GLU C 163 " pdb=" CD GLU C 163 " ideal model delta sigma weight residual 112.60 117.29 -4.69 1.70e+00 3.46e-01 7.62e+00 ... (remaining 19615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.67: 8468 32.67 - 65.34: 557 65.34 - 98.01: 45 98.01 - 130.68: 75 130.68 - 163.34: 15 Dihedral angle restraints: 9160 sinusoidal: 4460 harmonic: 4700 Sorted by residual: dihedral pdb=" C3 PEE B 409 " pdb=" C1 PEE B 409 " pdb=" C2 PEE B 409 " pdb=" O3P PEE B 409 " ideal model delta sinusoidal sigma weight residual 62.73 -133.93 -163.34 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C3 PEE C 409 " pdb=" C1 PEE C 409 " pdb=" C2 PEE C 409 " pdb=" O3P PEE C 409 " ideal model delta sinusoidal sigma weight residual 62.73 -133.98 -163.29 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C3 PEE A 409 " pdb=" C1 PEE A 409 " pdb=" C2 PEE A 409 " pdb=" O3P PEE A 409 " ideal model delta sinusoidal sigma weight residual 62.73 -134.00 -163.27 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 9157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 2039 0.120 - 0.241: 66 0.241 - 0.361: 10 0.361 - 0.481: 0 0.481 - 0.602: 5 Chirality restraints: 2120 Sorted by residual: chirality pdb=" CG LEU E 209 " pdb=" CB LEU E 209 " pdb=" CD1 LEU E 209 " pdb=" CD2 LEU E 209 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 9.05e+00 chirality pdb=" CG LEU C 209 " pdb=" CB LEU C 209 " pdb=" CD1 LEU C 209 " pdb=" CD2 LEU C 209 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 8.96e+00 chirality pdb=" CG LEU A 209 " pdb=" CB LEU A 209 " pdb=" CD1 LEU A 209 " pdb=" CD2 LEU A 209 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 8.91e+00 ... (remaining 2117 not shown) Planarity restraints: 2315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 213 " -0.011 2.00e-02 2.50e+03 2.73e-02 1.87e+01 pdb=" CG TRP D 213 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP D 213 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP D 213 " 0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP D 213 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP D 213 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP D 213 " 0.059 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 213 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 213 " -0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP D 213 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 213 " -0.011 2.00e-02 2.50e+03 2.72e-02 1.85e+01 pdb=" CG TRP E 213 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP E 213 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP E 213 " 0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP E 213 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP E 213 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP E 213 " 0.058 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 213 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 213 " -0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP E 213 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 213 " -0.011 2.00e-02 2.50e+03 2.71e-02 1.84e+01 pdb=" CG TRP C 213 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP C 213 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP C 213 " 0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP C 213 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 213 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP C 213 " 0.058 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 213 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 213 " -0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP C 213 " -0.005 2.00e-02 2.50e+03 ... (remaining 2312 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3003 2.79 - 3.32: 11966 3.32 - 3.85: 22228 3.85 - 4.37: 29057 4.37 - 4.90: 50506 Nonbonded interactions: 116760 Sorted by model distance: nonbonded pdb=" O LEU B 241 " pdb=" OG1 THR B 244 " model vdw 2.265 3.040 nonbonded pdb=" O LEU D 241 " pdb=" OG1 THR D 244 " model vdw 2.265 3.040 nonbonded pdb=" O LEU C 241 " pdb=" OG1 THR C 244 " model vdw 2.266 3.040 nonbonded pdb=" O LEU A 241 " pdb=" OG1 THR A 244 " model vdw 2.266 3.040 nonbonded pdb=" O LEU E 241 " pdb=" OG1 THR E 244 " model vdw 2.266 3.040 ... (remaining 116755 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' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or na \ me O5 or name P )) or resid 404 or (resid 405 through 406 and (name N or name C1 \ or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name C30 or na \ me C31 or name C32 or name C33 or name C4 or name C5 or name O1P or name O2 or n \ ame O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or \ (resid 407 through 408 and (name N or name C1 or name C10 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C4 or name C40 or name C5 or name O1P or name O2 or name O2 \ P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resi \ d 409 through 410 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22)))) selection = (chain 'B' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or na \ me O5 or name P )) or resid 404 or (resid 405 through 406 and (name N or name C1 \ or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name C30 or na \ me C31 or name C32 or name C33 or name C4 or name C5 or name O1P or name O2 or n \ ame O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or \ (resid 407 through 408 and (name N or name C1 or name C10 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C4 or name C40 or name C5 or name O1P or name O2 or name O2 \ P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resi \ d 409 through 410 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22)))) selection = (chain 'C' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or na \ me O5 or name P )) or resid 404 or (resid 405 through 406 and (name N or name C1 \ or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name C30 or na \ me C31 or name C32 or name C33 or name C4 or name C5 or name O1P or name O2 or n \ ame O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or \ (resid 407 through 408 and (name N or name C1 or name C10 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C4 or name C40 or name C5 or name O1P or name O2 or name O2 \ P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resi \ d 409 through 410 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22)))) selection = (chain 'D' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or na \ me O5 or name P )) or resid 404 or (resid 405 through 406 and (name N or name C1 \ or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name C30 or na \ me C31 or name C32 or name C33 or name C4 or name C5 or name O1P or name O2 or n \ ame O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or \ (resid 407 through 408 and (name N or name C1 or name C10 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C4 or name C40 or name C5 or name O1P or name O2 or name O2 \ P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resi \ d 409 through 410 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22)))) selection = (chain 'E' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or na \ me O5 or name P )) or (resid 404 and (name C1 or name C10 or name C11 or name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name O1P or name O2 or name O2P o \ r name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 4 \ 05 through 406 and (name N or name C1 or name C10 or name C11 or name C12 or nam \ e C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C4 o \ r name C5 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 o \ r name O4P or name O5 or name P )) or (resid 407 through 408 and (name N or name \ C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or n \ ame C16 or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 o \ r name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C3 \ 5 or name C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name \ C5 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name \ O4P or name O5 or name P )) or (resid 409 through 410 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)))) } 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.610 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.550 Find NCS groups from input model: 0.280 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 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 : 0.005 0.115 14640 Z= 0.232 Angle : 0.813 12.909 19620 Z= 0.430 Chirality : 0.065 0.602 2120 Planarity : 0.010 0.051 2315 Dihedral : 24.232 163.344 6100 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.14 % Allowed : 17.37 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.21), residues: 1555 helix: 2.73 (0.20), residues: 530 sheet: 0.73 (0.27), residues: 410 loop : -1.02 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.004 ARG E 287 TYR 0.050 0.008 TYR C 263 PHE 0.047 0.007 PHE E 207 TRP 0.059 0.012 TRP D 213 HIS 0.005 0.002 HIS E 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 (14640) covalent geometry : angle 0.81286 / 0.43 (19620) hydrogen bonds : bond 0.18261 / 12.43 ( 620) hydrogen bonds : angle 6.59688 / 4.37 ( 2080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.504 Fit side-chains REVERT: D 205 MET cc_start: 0.8031 (mmm) cc_final: 0.7809 (mmp) outliers start: 11 outliers final: 11 residues processed: 132 average time/residue: 0.6265 time to fit residues: 89.7056 Evaluate side-chains 116 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 219 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.0170 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.086481 restraints weight = 34518.780| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.67 r_work: 0.2767 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14640 Z= 0.171 Angle : 0.603 5.421 19620 Z= 0.308 Chirality : 0.046 0.145 2120 Planarity : 0.005 0.040 2315 Dihedral : 25.433 160.565 3167 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.28 % Allowed : 15.87 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.21), residues: 1555 helix: 3.22 (0.20), residues: 525 sheet: 0.70 (0.26), residues: 410 loop : -1.15 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 287 TYR 0.016 0.002 TYR C 102 PHE 0.011 0.001 PHE B 312 TRP 0.008 0.002 TRP E 47 HIS 0.001 0.001 HIS D 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (14640) covalent geometry : angle 0.60317 / 0.31 (19620) hydrogen bonds : bond 0.07796 / 5.17 ( 620) hydrogen bonds : angle 4.77953 / 3.21 ( 2080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.612 Fit side-chains REVERT: E 163 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: B 163 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7958 (mt-10) outliers start: 27 outliers final: 14 residues processed: 120 average time/residue: 0.5913 time to fit residues: 77.1516 Evaluate side-chains 114 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 292 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 0.0870 chunk 153 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 137 optimal weight: 0.0170 chunk 134 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.128104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.089424 restraints weight = 38610.632| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.86 r_work: 0.2818 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14640 Z= 0.114 Angle : 0.544 7.475 19620 Z= 0.271 Chirality : 0.044 0.142 2120 Planarity : 0.004 0.042 2315 Dihedral : 23.727 166.310 3160 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.85 % Allowed : 16.51 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.21), residues: 1555 helix: 3.46 (0.20), residues: 530 sheet: 0.45 (0.25), residues: 445 loop : -1.07 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 77 TYR 0.013 0.001 TYR C 102 PHE 0.007 0.001 PHE C 42 TRP 0.008 0.001 TRP A 47 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (14640) covalent geometry : angle 0.54432 / 0.27 (19620) hydrogen bonds : bond 0.06015 / 3.98 ( 620) hydrogen bonds : angle 4.33451 / 2.90 ( 2080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.364 Fit side-chains REVERT: E 14 GLU cc_start: 0.6641 (pm20) cc_final: 0.6363 (pm20) REVERT: A 14 GLU cc_start: 0.6528 (pm20) cc_final: 0.6143 (pm20) REVERT: B 163 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8048 (mt-10) REVERT: D 14 GLU cc_start: 0.6590 (pm20) cc_final: 0.6339 (pm20) outliers start: 21 outliers final: 14 residues processed: 119 average time/residue: 0.6568 time to fit residues: 84.4583 Evaluate side-chains 114 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 219 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 68 optimal weight: 8.9990 chunk 24 optimal weight: 0.0370 chunk 101 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.091919 restraints weight = 33475.328| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.70 r_work: 0.2862 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14640 Z= 0.104 Angle : 0.523 7.283 19620 Z= 0.259 Chirality : 0.044 0.169 2120 Planarity : 0.004 0.041 2315 Dihedral : 22.561 171.462 3160 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.35 % Allowed : 17.94 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.22), residues: 1555 helix: 3.40 (0.20), residues: 535 sheet: 0.45 (0.25), residues: 445 loop : -0.92 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 192 TYR 0.013 0.001 TYR C 102 PHE 0.006 0.001 PHE A 42 TRP 0.009 0.001 TRP B 47 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (14640) covalent geometry : angle 0.52252 / 0.26 (19620) hydrogen bonds : bond 0.05235 / 3.46 ( 620) hydrogen bonds : angle 4.04663 / 2.70 ( 2080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.422 Fit side-chains REVERT: E 14 GLU cc_start: 0.6597 (pm20) cc_final: 0.6278 (pm20) REVERT: A 14 GLU cc_start: 0.6543 (pm20) cc_final: 0.6175 (pm20) REVERT: D 14 GLU cc_start: 0.6621 (pm20) cc_final: 0.6388 (pm20) outliers start: 14 outliers final: 6 residues processed: 106 average time/residue: 0.6344 time to fit residues: 72.6525 Evaluate side-chains 104 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 107 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 0.0980 chunk 86 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.083798 restraints weight = 35969.353| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.72 r_work: 0.2712 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14640 Z= 0.236 Angle : 0.659 7.073 19620 Z= 0.334 Chirality : 0.049 0.176 2120 Planarity : 0.005 0.046 2315 Dihedral : 23.135 179.212 3155 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.21 % Allowed : 17.65 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.21), residues: 1555 helix: 3.11 (0.21), residues: 525 sheet: 0.42 (0.25), residues: 405 loop : -1.18 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 105 TYR 0.011 0.002 TYR C 102 PHE 0.009 0.002 PHE E 42 TRP 0.009 0.002 TRP C 213 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.24 (14640) covalent geometry : angle 0.65949 / 0.33 (19620) hydrogen bonds : bond 0.09191 / 6.09 ( 620) hydrogen bonds : angle 4.53197 / 3.04 ( 2080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.331 Fit side-chains REVERT: E 14 GLU cc_start: 0.6780 (pm20) cc_final: 0.6537 (pm20) REVERT: A 14 GLU cc_start: 0.6687 (pm20) cc_final: 0.6291 (pm20) REVERT: A 163 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8223 (mt-10) REVERT: C 14 GLU cc_start: 0.7261 (pm20) cc_final: 0.6979 (pm20) REVERT: C 287 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6923 (mtp180) REVERT: D 14 GLU cc_start: 0.6802 (pm20) cc_final: 0.6566 (pm20) outliers start: 26 outliers final: 19 residues processed: 111 average time/residue: 0.6553 time to fit residues: 78.5471 Evaluate side-chains 114 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 GLN B 284 GLN D 284 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.084042 restraints weight = 34888.226| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.68 r_work: 0.2725 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14640 Z= 0.219 Angle : 0.645 6.793 19620 Z= 0.324 Chirality : 0.048 0.185 2120 Planarity : 0.005 0.047 2315 Dihedral : 23.114 172.376 3155 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.28 % Allowed : 17.30 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.21), residues: 1555 helix: 3.05 (0.21), residues: 525 sheet: 0.40 (0.25), residues: 405 loop : -1.22 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 77 TYR 0.012 0.002 TYR C 102 PHE 0.010 0.001 PHE A 312 TRP 0.007 0.001 TRP C 213 HIS 0.002 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.22 (14640) covalent geometry : angle 0.64542 / 0.32 (19620) hydrogen bonds : bond 0.08840 / 5.85 ( 620) hydrogen bonds : angle 4.53418 / 3.03 ( 2080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.382 Fit side-chains REVERT: E 14 GLU cc_start: 0.6790 (pm20) cc_final: 0.6502 (pm20) REVERT: A 14 GLU cc_start: 0.6761 (pm20) cc_final: 0.6354 (pm20) REVERT: A 163 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8224 (mt-10) REVERT: C 14 GLU cc_start: 0.7221 (pm20) cc_final: 0.6981 (pm20) REVERT: C 287 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.6928 (mtp180) REVERT: D 14 GLU cc_start: 0.6826 (pm20) cc_final: 0.6598 (pm20) outliers start: 27 outliers final: 19 residues processed: 107 average time/residue: 0.6827 time to fit residues: 79.0250 Evaluate side-chains 112 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 65 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 GLN B 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.088197 restraints weight = 32440.087| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.63 r_work: 0.2792 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14640 Z= 0.126 Angle : 0.563 6.795 19620 Z= 0.281 Chirality : 0.045 0.190 2120 Planarity : 0.004 0.045 2315 Dihedral : 22.369 174.016 3155 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.99 % Allowed : 17.72 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.21), residues: 1555 helix: 2.94 (0.20), residues: 560 sheet: 0.48 (0.25), residues: 410 loop : -1.15 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 192 TYR 0.013 0.001 TYR A 102 PHE 0.009 0.001 PHE E 312 TRP 0.007 0.001 TRP A 47 HIS 0.002 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (14640) covalent geometry : angle 0.56295 / 0.28 (19620) hydrogen bonds : bond 0.06673 / 4.42 ( 620) hydrogen bonds : angle 4.27373 / 2.85 ( 2080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.393 Fit side-chains REVERT: E 14 GLU cc_start: 0.6730 (pm20) cc_final: 0.6454 (pm20) REVERT: A 14 GLU cc_start: 0.6713 (pm20) cc_final: 0.6329 (pm20) REVERT: A 93 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.8108 (m) REVERT: A 163 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8251 (mt-10) REVERT: C 14 GLU cc_start: 0.7236 (pm20) cc_final: 0.6927 (pm20) REVERT: C 287 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6694 (mtp180) REVERT: D 14 GLU cc_start: 0.6772 (pm20) cc_final: 0.6553 (pm20) outliers start: 23 outliers final: 15 residues processed: 109 average time/residue: 0.6647 time to fit residues: 78.4171 Evaluate side-chains 110 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 292 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.086764 restraints weight = 31426.936| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.57 r_work: 0.2768 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14640 Z= 0.163 Angle : 0.595 6.750 19620 Z= 0.298 Chirality : 0.046 0.192 2120 Planarity : 0.004 0.046 2315 Dihedral : 22.348 171.567 3155 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.21 % Allowed : 17.44 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.21), residues: 1555 helix: 3.25 (0.20), residues: 530 sheet: 0.47 (0.25), residues: 410 loop : -1.18 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 77 TYR 0.012 0.001 TYR C 102 PHE 0.008 0.001 PHE A 42 TRP 0.005 0.001 TRP A 47 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (14640) covalent geometry : angle 0.59506 / 0.30 (19620) hydrogen bonds : bond 0.07612 / 5.04 ( 620) hydrogen bonds : angle 4.32957 / 2.89 ( 2080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.375 Fit side-chains REVERT: E 14 GLU cc_start: 0.6776 (pm20) cc_final: 0.6503 (pm20) REVERT: A 14 GLU cc_start: 0.6746 (pm20) cc_final: 0.6347 (pm20) REVERT: A 163 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: C 14 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6925 (pm20) REVERT: C 287 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.6850 (mtp180) REVERT: D 14 GLU cc_start: 0.6792 (pm20) cc_final: 0.6590 (pm20) outliers start: 26 outliers final: 22 residues processed: 108 average time/residue: 0.6423 time to fit residues: 75.0066 Evaluate side-chains 115 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 292 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 11 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.088557 restraints weight = 35478.871| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.75 r_work: 0.2796 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14640 Z= 0.126 Angle : 0.556 6.790 19620 Z= 0.277 Chirality : 0.045 0.194 2120 Planarity : 0.004 0.046 2315 Dihedral : 21.910 172.220 3155 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.92 % Allowed : 17.79 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.21), residues: 1555 helix: 3.38 (0.20), residues: 530 sheet: 0.48 (0.25), residues: 410 loop : -1.14 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 192 TYR 0.014 0.001 TYR D 102 PHE 0.009 0.001 PHE C 312 TRP 0.007 0.001 TRP A 47 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (14640) covalent geometry : angle 0.55612 / 0.28 (19620) hydrogen bonds : bond 0.06386 / 4.23 ( 620) hydrogen bonds : angle 4.17332 / 2.78 ( 2080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.525 Fit side-chains REVERT: E 14 GLU cc_start: 0.6736 (pm20) cc_final: 0.6461 (pm20) REVERT: A 14 GLU cc_start: 0.6691 (pm20) cc_final: 0.6297 (pm20) REVERT: A 93 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.8107 (m) REVERT: A 163 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8262 (mt-10) REVERT: C 14 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6907 (pm20) REVERT: C 287 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6653 (mtp180) REVERT: D 14 GLU cc_start: 0.6748 (pm20) cc_final: 0.6534 (pm20) outliers start: 22 outliers final: 14 residues processed: 102 average time/residue: 0.7061 time to fit residues: 77.5350 Evaluate side-chains 109 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 292 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 71 optimal weight: 7.9990 chunk 152 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.090626 restraints weight = 36526.497| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.80 r_work: 0.2842 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14640 Z= 0.111 Angle : 0.541 9.656 19620 Z= 0.269 Chirality : 0.045 0.195 2120 Planarity : 0.004 0.045 2315 Dihedral : 21.324 173.783 3155 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.71 % Allowed : 18.08 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.21), residues: 1555 helix: 3.34 (0.20), residues: 535 sheet: 0.44 (0.24), residues: 445 loop : -0.99 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 50 TYR 0.014 0.001 TYR D 102 PHE 0.008 0.001 PHE A 42 TRP 0.008 0.001 TRP A 47 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14640) covalent geometry : angle 0.54075 / 0.27 (19620) hydrogen bonds : bond 0.05485 / 3.63 ( 620) hydrogen bonds : angle 3.98795 / 2.65 ( 2080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.510 Fit side-chains REVERT: E 14 GLU cc_start: 0.6711 (pm20) cc_final: 0.6431 (pm20) REVERT: A 14 GLU cc_start: 0.6601 (pm20) cc_final: 0.6231 (pm20) REVERT: A 93 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.8080 (m) REVERT: A 163 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8272 (mt-10) REVERT: B 101 GLN cc_start: 0.8339 (mt0) cc_final: 0.8044 (mt0) REVERT: C 14 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: C 287 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6617 (mtp180) outliers start: 19 outliers final: 12 residues processed: 106 average time/residue: 0.6535 time to fit residues: 75.1495 Evaluate side-chains 109 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 292 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.125223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.087609 restraints weight = 30123.554| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.52 r_work: 0.2782 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14640 Z= 0.160 Angle : 0.590 6.764 19620 Z= 0.297 Chirality : 0.046 0.198 2120 Planarity : 0.004 0.046 2315 Dihedral : 21.559 173.724 3155 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.78 % Allowed : 17.86 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.21), residues: 1555 helix: 3.20 (0.21), residues: 530 sheet: 0.45 (0.25), residues: 410 loop : -1.08 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 50 TYR 0.012 0.001 TYR C 102 PHE 0.008 0.001 PHE B 42 TRP 0.005 0.001 TRP A 47 HIS 0.001 0.001 HIS E 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (14640) covalent geometry : angle 0.58994 / 0.30 (19620) hydrogen bonds : bond 0.07407 / 4.90 ( 620) hydrogen bonds : angle 4.21484 / 2.81 ( 2080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3529.80 seconds wall clock time: 60 minutes 58.00 seconds (3658.00 seconds total)