Starting phenix.real_space_refine on Thu Feb 5 01:42:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcr_37447/02_2026/8wcr_37447.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcr_37447/02_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_37447/02_2026/8wcr_37447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcr_37447/02_2026/8wcr_37447.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wcr_37447/02_2026/8wcr_37447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcr_37447/02_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-2.0-5952/lib/python3.9/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, 332 Unusual residues: {' CL': 1, 'PEE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} 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, 332 Unusual residues: {' CL': 1, 'PEE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} 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, 332 Unusual residues: {' CL': 1, 'PEE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} 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, 332 Unusual residues: {' CL': 1, 'PEE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} 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, 332 Unusual residues: {' CL': 1, 'PEE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} 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: 4.92, per 1000 atoms: 0.34 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: 1.28 Conformation dependent library (CDL) restraints added in 807.0 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: 0.47 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: 2.55 Time building geometry restraints manager: 1.60 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: 2.290 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.400 Find NCS groups from input model: 0.400 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: 0.010 Load rotamer database and sin/cos tables:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 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 covalent geometry : bond 0.00502 (14640) covalent geometry : angle 0.81286 (19620) hydrogen bonds : bond 0.18261 ( 620) hydrogen bonds : angle 6.59688 ( 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 : 0.510 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: 0.7811 time to fit residues: 111.3893 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 : 0.594 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 37)----------------| | 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: 0.2766 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 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 = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 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 covalent geometry : bond 0.00408 (14640) covalent geometry : angle 0.60317 (19620) hydrogen bonds : bond 0.07796 ( 620) hydrogen bonds : angle 4.77953 ( 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 : 0.589 Fit side-chains REVERT: E 163 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: B 163 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7959 (mt-10) outliers start: 27 outliers final: 14 residues processed: 120 average time/residue: 0.7895 time to fit residues: 102.5358 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 : 0.530 ------------------------------------------------------------------------------- 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: 0.0970 chunk 153 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 137 optimal weight: 0.0770 chunk 134 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.091893 restraints weight = 38518.800| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.86 r_work: 0.2862 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1030 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= 0.105 Angle : 0.532 7.314 19620 Z= 0.265 Chirality : 0.044 0.142 2120 Planarity : 0.004 0.041 2315 Dihedral : 23.352 166.427 3160 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.49 % Allowed : 16.87 % 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: 1.48 (0.21), residues: 1555 helix: 3.47 (0.20), residues: 530 sheet: 0.44 (0.25), residues: 445 loop : -1.01 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 109 TYR 0.014 0.001 TYR C 102 PHE 0.006 0.001 PHE E 106 TRP 0.009 0.001 TRP A 47 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00216 (14640) covalent geometry : angle 0.53225 (19620) hydrogen bonds : bond 0.05212 ( 620) hydrogen bonds : angle 4.21512 ( 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 135 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.587 Fit side-chains REVERT: E 14 GLU cc_start: 0.6609 (pm20) cc_final: 0.6322 (pm20) REVERT: A 14 GLU cc_start: 0.6500 (pm20) cc_final: 0.6122 (pm20) REVERT: B 163 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: D 14 GLU cc_start: 0.6574 (pm20) cc_final: 0.6335 (pm20) outliers start: 16 outliers final: 7 residues processed: 122 average time/residue: 0.8358 time to fit residues: 110.0033 Evaluate side-chains 104 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 261 MET 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 B residue 163 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 68 optimal weight: 4.9990 chunk 24 optimal weight: 0.0030 chunk 101 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 112 optimal weight: 0.0270 chunk 103 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 1.1650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.089817 restraints weight = 33571.954| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.68 r_work: 0.2821 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14640 Z= 0.122 Angle : 0.547 8.283 19620 Z= 0.272 Chirality : 0.044 0.170 2120 Planarity : 0.004 0.041 2315 Dihedral : 22.647 172.214 3155 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.42 % Allowed : 18.15 % 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: 1.45 (0.21), residues: 1555 helix: 3.35 (0.21), residues: 530 sheet: 0.42 (0.25), residues: 445 loop : -0.92 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 192 TYR 0.012 0.001 TYR C 102 PHE 0.008 0.001 PHE B 42 TRP 0.007 0.001 TRP A 47 HIS 0.002 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00270 (14640) covalent geometry : angle 0.54681 (19620) hydrogen bonds : bond 0.06134 ( 620) hydrogen bonds : angle 4.14880 ( 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 115 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.568 Fit side-chains REVERT: E 14 GLU cc_start: 0.6635 (pm20) cc_final: 0.6303 (pm20) REVERT: A 14 GLU cc_start: 0.6556 (pm20) cc_final: 0.6176 (pm20) REVERT: B 14 GLU cc_start: 0.7331 (pm20) cc_final: 0.7118 (pm20) REVERT: D 14 GLU cc_start: 0.6646 (pm20) cc_final: 0.6396 (pm20) outliers start: 15 outliers final: 9 residues processed: 104 average time/residue: 0.9150 time to fit residues: 101.9040 Evaluate side-chains 107 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 GLN 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 B residue 101 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B 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: 2.9990 chunk 16 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 128 optimal weight: 0.0470 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 overall best weight: 1.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.087844 restraints weight = 35838.176| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.75 r_work: 0.2786 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14640 Z= 0.135 Angle : 0.559 8.146 19620 Z= 0.279 Chirality : 0.045 0.184 2120 Planarity : 0.004 0.043 2315 Dihedral : 22.146 179.372 3155 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.64 % Allowed : 17.94 % 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: 1.37 (0.21), residues: 1555 helix: 3.37 (0.20), residues: 525 sheet: 0.38 (0.24), residues: 445 loop : -1.04 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 192 TYR 0.012 0.001 TYR C 102 PHE 0.008 0.001 PHE E 42 TRP 0.005 0.001 TRP A 47 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00307 (14640) covalent geometry : angle 0.55890 (19620) hydrogen bonds : bond 0.06761 ( 620) hydrogen bonds : angle 4.19390 ( 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 115 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.547 Fit side-chains REVERT: E 14 GLU cc_start: 0.6655 (pm20) cc_final: 0.6392 (pm20) REVERT: A 14 GLU cc_start: 0.6591 (pm20) cc_final: 0.6207 (pm20) REVERT: A 163 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8236 (mt-10) REVERT: B 14 GLU cc_start: 0.7120 (pm20) cc_final: 0.6864 (pm20) REVERT: C 287 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6713 (mtp180) REVERT: D 14 GLU cc_start: 0.6672 (pm20) cc_final: 0.6468 (pm20) outliers start: 18 outliers final: 12 residues processed: 101 average time/residue: 0.9103 time to fit residues: 98.6160 Evaluate side-chains 106 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 LEU 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 163 GLU Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 287 ARG 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: 7.9990 chunk 31 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.084996 restraints weight = 34968.109| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.71 r_work: 0.2734 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14640 Z= 0.202 Angle : 0.625 8.124 19620 Z= 0.313 Chirality : 0.047 0.189 2120 Planarity : 0.004 0.045 2315 Dihedral : 22.410 173.304 3155 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.06 % Allowed : 17.58 % 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: 1.21 (0.21), residues: 1555 helix: 3.21 (0.21), residues: 525 sheet: 0.44 (0.25), residues: 410 loop : -1.14 (0.23), residues: 620 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 0.008 0.001 PHE B 42 TRP 0.007 0.001 TRP C 213 HIS 0.002 0.001 HIS C 127 Details of bonding type rmsd covalent geometry : bond 0.00494 (14640) covalent geometry : angle 0.62471 (19620) hydrogen bonds : bond 0.08489 ( 620) hydrogen bonds : angle 4.40148 ( 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 123 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.492 Fit side-chains REVERT: E 14 GLU cc_start: 0.6749 (pm20) cc_final: 0.6483 (pm20) REVERT: A 14 GLU cc_start: 0.6677 (pm20) cc_final: 0.6294 (pm20) REVERT: A 163 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8223 (mt-10) REVERT: B 14 GLU cc_start: 0.7280 (pm20) cc_final: 0.7037 (pm20) REVERT: C 287 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6887 (mtp180) outliers start: 24 outliers final: 19 residues processed: 109 average time/residue: 0.8764 time to fit residues: 102.5700 Evaluate side-chains 115 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 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 163 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 65 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 284 GLN D 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.089569 restraints weight = 32493.314| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.63 r_work: 0.2815 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14640 Z= 0.118 Angle : 0.550 7.875 19620 Z= 0.274 Chirality : 0.045 0.190 2120 Planarity : 0.004 0.044 2315 Dihedral : 21.773 174.118 3155 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.71 % Allowed : 18.01 % 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: 1.42 (0.21), residues: 1555 helix: 3.40 (0.20), residues: 530 sheet: 0.42 (0.24), residues: 445 loop : -1.05 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 192 TYR 0.013 0.001 TYR C 102 PHE 0.008 0.001 PHE B 42 TRP 0.007 0.001 TRP D 47 HIS 0.001 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00255 (14640) covalent geometry : angle 0.55048 (19620) hydrogen bonds : bond 0.06137 ( 620) hydrogen bonds : angle 4.15768 ( 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 116 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.526 Fit side-chains REVERT: E 14 GLU cc_start: 0.6680 (pm20) cc_final: 0.6430 (pm20) REVERT: A 14 GLU cc_start: 0.6615 (pm20) cc_final: 0.6250 (pm20) REVERT: B 14 GLU cc_start: 0.7211 (pm20) cc_final: 0.6960 (pm20) REVERT: C 287 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6639 (mtp180) outliers start: 19 outliers final: 15 residues processed: 104 average time/residue: 0.8718 time to fit residues: 97.3230 Evaluate side-chains 110 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 261 MET Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 287 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 14 optimal weight: 7.9990 chunk 7 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.086994 restraints weight = 31482.577| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.58 r_work: 0.2771 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1284 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= 0.162 Angle : 0.590 7.957 19620 Z= 0.295 Chirality : 0.046 0.191 2120 Planarity : 0.004 0.044 2315 Dihedral : 21.881 171.035 3155 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.14 % Allowed : 17.15 % 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: 1.28 (0.21), residues: 1555 helix: 3.19 (0.21), residues: 530 sheet: 0.47 (0.25), residues: 410 loop : -1.06 (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 B 42 TRP 0.005 0.001 TRP C 213 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00386 (14640) covalent geometry : angle 0.58960 (19620) hydrogen bonds : bond 0.07522 ( 620) hydrogen bonds : angle 4.27843 ( 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 121 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.520 Fit side-chains REVERT: E 14 GLU cc_start: 0.6715 (pm20) cc_final: 0.6465 (pm20) REVERT: A 14 GLU cc_start: 0.6649 (pm20) cc_final: 0.6285 (pm20) REVERT: A 163 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8221 (mt-10) REVERT: B 14 GLU cc_start: 0.7195 (pm20) cc_final: 0.6959 (pm20) REVERT: C 287 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6812 (mtp180) outliers start: 25 outliers final: 21 residues processed: 109 average time/residue: 0.8369 time to fit residues: 98.4404 Evaluate side-chains 116 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 219 THR Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain A residue 39 VAL 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 219 THR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 287 ARG 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 11 optimal weight: 0.0980 chunk 130 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.127159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.088593 restraints weight = 35552.290| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.75 r_work: 0.2798 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 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 = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1272 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= 0.128 Angle : 0.555 7.871 19620 Z= 0.276 Chirality : 0.045 0.191 2120 Planarity : 0.004 0.045 2315 Dihedral : 21.552 171.301 3155 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.92 % Allowed : 17.37 % 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: 1.36 (0.21), residues: 1555 helix: 3.38 (0.20), residues: 530 sheet: 0.48 (0.25), residues: 410 loop : -1.11 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 50 TYR 0.012 0.001 TYR A 102 PHE 0.008 0.001 PHE A 42 TRP 0.006 0.001 TRP A 47 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00290 (14640) covalent geometry : angle 0.55465 (19620) hydrogen bonds : bond 0.06414 ( 620) hydrogen bonds : angle 4.15211 ( 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 116 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.568 Fit side-chains REVERT: E 14 GLU cc_start: 0.6701 (pm20) cc_final: 0.6463 (pm20) REVERT: A 14 GLU cc_start: 0.6607 (pm20) cc_final: 0.6248 (pm20) REVERT: A 163 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: B 14 GLU cc_start: 0.7210 (pm20) cc_final: 0.6971 (pm20) REVERT: C 287 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6665 (mtp180) outliers start: 22 outliers final: 19 residues processed: 104 average time/residue: 0.8593 time to fit residues: 96.2308 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 : 0.556 ------------------------------------------------------------------------------- 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 219 THR Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain A residue 39 VAL 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 219 THR Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 287 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 71 optimal weight: 8.9990 chunk 152 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.129117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090555 restraints weight = 36543.891| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.79 r_work: 0.2833 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14640 Z= 0.111 Angle : 0.536 8.012 19620 Z= 0.265 Chirality : 0.044 0.191 2120 Planarity : 0.004 0.044 2315 Dihedral : 21.059 171.977 3155 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.85 % Allowed : 17.44 % 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: 1.45 (0.21), residues: 1555 helix: 3.35 (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 0.013 0.001 TYR D 102 PHE 0.014 0.001 PHE C 312 TRP 0.008 0.001 TRP A 47 HIS 0.002 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00245 (14640) covalent geometry : angle 0.53598 (19620) hydrogen bonds : bond 0.05581 ( 620) hydrogen bonds : angle 3.98680 ( 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 119 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.483 Fit side-chains REVERT: E 14 GLU cc_start: 0.6616 (pm20) cc_final: 0.6379 (pm20) REVERT: A 14 GLU cc_start: 0.6558 (pm20) cc_final: 0.6266 (pm20) REVERT: A 163 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8247 (mt-10) REVERT: B 14 GLU cc_start: 0.7194 (pm20) cc_final: 0.6946 (pm20) REVERT: C 287 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6599 (mtp180) outliers start: 21 outliers final: 14 residues processed: 108 average time/residue: 0.8464 time to fit residues: 98.9376 Evaluate side-chains 111 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 219 THR Chi-restraints excluded: chain E residue 261 MET 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 219 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 191 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 99 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.086870 restraints weight = 30200.625| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.53 r_work: 0.2770 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1364 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= 0.171 Angle : 0.594 7.923 19620 Z= 0.298 Chirality : 0.046 0.194 2120 Planarity : 0.004 0.044 2315 Dihedral : 21.451 170.948 3155 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.71 % Allowed : 17.51 % Favored : 80.78 % 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: 1.24 (0.21), residues: 1555 helix: 3.25 (0.21), residues: 525 sheet: 0.45 (0.25), residues: 410 loop : -1.12 (0.24), residues: 620 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 D 42 TRP 0.005 0.001 TRP B 213 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00411 (14640) covalent geometry : angle 0.59384 (19620) hydrogen bonds : bond 0.07803 ( 620) hydrogen bonds : angle 4.27137 ( 2080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4488.78 seconds wall clock time: 77 minutes 24.07 seconds (4644.07 seconds total)