Starting phenix.real_space_refine on Thu Feb 5 01:47:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jj3_36339/02_2026/8jj3_36339.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jj3_36339/02_2026/8jj3_36339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6476 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jj3_36339/02_2026/8jj3_36339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jj3_36339/02_2026/8jj3_36339.map" model { file = "/net/cci-nas-00/data/ceres_data/8jj3_36339/02_2026/8jj3_36339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jj3_36339/02_2026/8jj3_36339.cif" } resolution = 2.6476 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 9635 2.51 5 N 2075 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 20 residue(s): 0.02s 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: 14635 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2540 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: 2585 Chain: "C" Number of atoms: 2540 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: 2585 Chain: "B" Number of atoms: 2540 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: 2585 Chain: "D" Number of atoms: 2540 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: 2585 Chain: "E" Number of atoms: 2540 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: 2585 Chain: "A" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 334 Unusual residues: {' CL': 1, 'PEE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 128 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: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 334 Unusual residues: {' CL': 1, 'PEE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 128 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: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 334 Unusual residues: {' CL': 1, 'PEE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 128 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: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 334 Unusual residues: {' CL': 1, 'PEE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 128 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: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 334 Unusual residues: {' CL': 1, 'PEE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 128 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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AARG A 293 " occ=0.61 ... (20 atoms not shown) pdb=" NH2BARG A 293 " occ=0.39 residue: pdb=" N AARG C 293 " occ=0.61 ... (20 atoms not shown) pdb=" NH2BARG C 293 " occ=0.39 residue: pdb=" N AARG B 293 " occ=0.61 ... (20 atoms not shown) pdb=" NH2BARG B 293 " occ=0.39 residue: pdb=" N AARG D 293 " occ=0.61 ... (20 atoms not shown) pdb=" NH2BARG D 293 " occ=0.39 residue: pdb=" N AARG E 293 " occ=0.61 ... (20 atoms not shown) pdb=" NH2BARG E 293 " occ=0.39 Time building chain proxies: 4.55, per 1000 atoms: 0.31 Number of scatterers: 14635 At special positions: 0 Unit cell: (91.8488, 91.8488, 127.902, 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 2075 7.00 C 9635 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: 1.02 Conformation dependent library (CDL) restraints added in 887.9 milliseconds 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 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: 40 helices and 20 sheets defined 39.7% alpha, 51.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 50 through 53 removed outlier: 3.525A pdb=" N ALA A 53 " --> pdb=" O ARG A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 50 through 53' Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.513A pdb=" N SER A 59 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 196 through 213 removed outlier: 5.500A 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: 3.565A pdb=" N TRP A 217 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 218' Processing helix chain 'A' and resid 220 through 243 Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 316 removed outlier: 3.815A pdb=" N ILE A 297 " --> pdb=" O AARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'C' and resid 50 through 53 removed outlier: 3.525A pdb=" N ALA C 53 " --> pdb=" O ARG C 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 50 through 53' Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.513A pdb=" N SER C 59 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 196 through 213 removed outlier: 5.500A 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: 3.565A pdb=" N TRP C 217 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 214 through 218' Processing helix chain 'C' and resid 220 through 243 Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 284 through 316 removed outlier: 3.815A pdb=" N ILE C 297 " --> pdb=" O AARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'B' and resid 50 through 53 removed outlier: 3.524A pdb=" N ALA B 53 " --> pdb=" O ARG B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 53' Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.513A pdb=" N SER B 59 " --> pdb=" O ASP B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 196 through 213 removed outlier: 5.501A 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: 3.565A pdb=" N TRP B 217 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 214 through 218' Processing helix chain 'B' and resid 220 through 243 Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 284 through 316 removed outlier: 3.810A pdb=" N ILE B 297 " --> pdb=" O AARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'D' and resid 50 through 53 removed outlier: 3.524A pdb=" N ALA D 53 " --> pdb=" O ARG D 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 50 through 53' Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.512A pdb=" N SER D 59 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 196 through 213 removed outlier: 5.501A 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: 3.565A pdb=" N TRP D 217 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER D 218 " --> pdb=" O ALA D 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 214 through 218' Processing helix chain 'D' and resid 220 through 243 Processing helix chain 'D' and resid 253 through 282 Processing helix chain 'D' and resid 284 through 316 removed outlier: 3.815A pdb=" N ILE D 297 " --> pdb=" O AARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing helix chain 'E' and resid 50 through 53 removed outlier: 3.525A pdb=" N ALA E 53 " --> pdb=" O ARG E 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 50 through 53' Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.513A pdb=" N SER E 59 " --> pdb=" O ASP E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 196 through 213 removed outlier: 5.501A 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: 3.565A pdb=" N TRP E 217 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER E 218 " --> pdb=" O ALA E 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 214 through 218' Processing helix chain 'E' and resid 220 through 243 Processing helix chain 'E' and resid 253 through 282 Processing helix chain 'E' and resid 284 through 316 removed outlier: 3.815A pdb=" N ILE E 297 " --> pdb=" O AARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 5.648A pdb=" N ALA A 87 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N SER A 107 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP A 47 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 38 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER A 29 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASN A 40 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 27 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N PHE A 42 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE A 25 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N SER A 44 " --> pdb=" O TYR A 23 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N TYR A 23 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N SER A 46 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N GLY A 21 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N LYS A 48 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N ASN A 19 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU A 16 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA A 143 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL A 18 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 removed outlier: 5.648A pdb=" N ALA A 87 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N SER A 107 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP A 47 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 38 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER A 29 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASN A 40 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS A 27 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N PHE A 42 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE A 25 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N SER A 44 " --> pdb=" O TYR A 23 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N TYR A 23 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N SER A 46 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N GLY A 21 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N LYS A 48 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N ASN A 19 " --> pdb=" O LYS A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 7.313A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 64 through 65 removed outlier: 5.648A pdb=" N ALA C 87 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N SER C 107 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP C 47 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 38 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER C 29 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASN C 40 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N CYS C 27 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N PHE C 42 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE C 25 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N SER C 44 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N TYR C 23 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N SER C 46 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLY C 21 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N LYS C 48 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N ASN C 19 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 64 through 65 removed outlier: 5.648A pdb=" N ALA C 87 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N SER C 107 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP C 47 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 38 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER C 29 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASN C 40 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N CYS C 27 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N PHE C 42 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE C 25 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N SER C 44 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N TYR C 23 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N SER C 46 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLY C 21 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N LYS C 48 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N ASN C 19 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 76 through 78 removed outlier: 7.312A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78 Processing sheet with id=AA9, first strand: chain 'B' and resid 64 through 65 removed outlier: 5.648A pdb=" N ALA B 87 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N SER B 107 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP B 47 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 38 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER B 29 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASN B 40 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N CYS B 27 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N PHE B 42 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE B 25 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N SER B 44 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N TYR B 23 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N SER B 46 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N GLY B 21 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N LYS B 48 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N ASN B 19 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA B 143 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 65 removed outlier: 5.648A pdb=" N ALA B 87 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N SER B 107 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP B 47 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 38 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER B 29 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASN B 40 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N CYS B 27 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N PHE B 42 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE B 25 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N SER B 44 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N TYR B 23 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N SER B 46 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N GLY B 21 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N LYS B 48 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N ASN B 19 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 76 through 78 removed outlier: 7.313A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 76 through 78 Processing sheet with id=AB4, first strand: chain 'D' and resid 64 through 65 removed outlier: 5.648A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP D 47 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS D 38 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N SER D 29 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASN D 40 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N CYS D 27 " --> pdb=" O ASN D 40 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N PHE D 42 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE D 25 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N SER D 44 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N TYR D 23 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N SER D 46 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLY D 21 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N LYS D 48 " --> pdb=" O ASN D 19 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N ASN D 19 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA D 143 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 6.208A 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: 5.648A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP D 47 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS D 38 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N SER D 29 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASN D 40 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N CYS D 27 " --> pdb=" O ASN D 40 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N PHE D 42 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE D 25 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N SER D 44 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N TYR D 23 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N SER D 46 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLY D 21 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N LYS D 48 " --> pdb=" O ASN D 19 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N ASN D 19 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 7.312A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AB8, first strand: chain 'E' and resid 64 through 65 removed outlier: 5.648A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP E 47 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS E 38 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N SER E 29 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASN E 40 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS E 27 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N PHE E 42 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE E 25 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N SER E 44 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N TYR E 23 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N SER E 46 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLY E 21 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N LYS E 48 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N ASN E 19 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 64 through 65 removed outlier: 5.648A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP E 47 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS E 38 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N SER E 29 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASN E 40 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS E 27 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N PHE E 42 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE E 25 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N SER E 44 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N TYR E 23 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N SER E 46 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N GLY E 21 " --> pdb=" O SER E 46 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N LYS E 48 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N ASN E 19 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 removed outlier: 7.312A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78 775 hydrogen bonds defined for protein. 2210 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: 2.31 Time building geometry restraints manager: 1.39 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: 2161 1.32 - 1.44: 3837 1.44 - 1.56: 8547 1.56 - 1.69: 85 1.69 - 1.81: 35 Bond restraints: 14665 Sorted by residual: bond pdb=" CD BARG D 293 " pdb=" NE BARG D 293 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.40e-02 5.10e+03 9.04e+00 bond pdb=" CG LYS B 248 " pdb=" CD LYS B 248 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 5.05e+00 bond pdb=" CG LYS D 248 " pdb=" CD LYS D 248 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 5.04e+00 bond pdb=" CA AARG B 293 " pdb=" C AARG B 293 " ideal model delta sigma weight residual 1.524 1.552 -0.029 1.29e-02 6.01e+03 5.04e+00 bond pdb=" CG LYS E 248 " pdb=" CD LYS E 248 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 4.97e+00 ... (remaining 14660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 18931 2.05 - 4.10: 592 4.10 - 6.15: 109 6.15 - 8.19: 13 8.19 - 10.24: 5 Bond angle restraints: 19650 Sorted by residual: angle pdb=" NE BARG D 293 " pdb=" CZ BARG D 293 " pdb=" NH2BARG D 293 " ideal model delta sigma weight residual 119.20 115.66 3.54 9.00e-01 1.23e+00 1.55e+01 angle pdb=" NE BARG D 293 " pdb=" CZ BARG D 293 " pdb=" NH1BARG D 293 " ideal model delta sigma weight residual 121.50 125.26 -3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CD BARG D 293 " pdb=" NE BARG D 293 " pdb=" CZ BARG D 293 " ideal model delta sigma weight residual 124.40 119.18 5.22 1.40e+00 5.10e-01 1.39e+01 angle pdb=" C AARG D 293 " pdb=" CA AARG D 293 " pdb=" CB AARG D 293 " ideal model delta sigma weight residual 110.85 116.99 -6.14 1.70e+00 3.46e-01 1.31e+01 angle pdb=" C PHE A 78 " pdb=" N VAL A 79 " pdb=" CA VAL A 79 " ideal model delta sigma weight residual 122.35 118.32 4.03 1.18e+00 7.18e-01 1.17e+01 ... (remaining 19645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.36: 8490 32.36 - 64.73: 500 64.73 - 97.09: 50 97.09 - 129.45: 50 129.45 - 161.82: 80 Dihedral angle restraints: 9170 sinusoidal: 4470 harmonic: 4700 Sorted by residual: dihedral pdb=" C4 PEE E 401 " pdb=" O4P PEE E 401 " pdb=" P PEE E 401 " pdb=" O2P PEE E 401 " ideal model delta sinusoidal sigma weight residual -75.78 86.04 -161.82 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C4 PEE B 401 " pdb=" O4P PEE B 401 " pdb=" P PEE B 401 " pdb=" O2P PEE B 401 " ideal model delta sinusoidal sigma weight residual -75.78 86.02 -161.80 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C4 PEE C 410 " pdb=" O4P PEE C 410 " pdb=" P PEE C 410 " pdb=" O2P PEE C 410 " ideal model delta sinusoidal sigma weight residual -75.78 85.99 -161.77 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 9167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 2037 0.126 - 0.252: 78 0.252 - 0.377: 0 0.377 - 0.503: 0 0.503 - 0.629: 5 Chirality restraints: 2120 Sorted by residual: chirality pdb=" CG LEU B 180 " pdb=" CB LEU B 180 " pdb=" CD1 LEU B 180 " pdb=" CD2 LEU B 180 " both_signs ideal model delta sigma weight residual False -2.59 -1.96 -0.63 2.00e-01 2.50e+01 9.89e+00 chirality pdb=" CG LEU A 180 " pdb=" CB LEU A 180 " pdb=" CD1 LEU A 180 " pdb=" CD2 LEU A 180 " both_signs ideal model delta sigma weight residual False -2.59 -1.96 -0.63 2.00e-01 2.50e+01 9.87e+00 chirality pdb=" CG LEU D 180 " pdb=" CB LEU D 180 " pdb=" CD1 LEU D 180 " pdb=" CD2 LEU D 180 " both_signs ideal model delta sigma weight residual False -2.59 -1.96 -0.63 2.00e-01 2.50e+01 9.85e+00 ... (remaining 2117 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA AARG B 293 " -0.029 2.00e-02 2.50e+03 5.88e-02 3.45e+01 pdb=" C AARG B 293 " 0.102 2.00e-02 2.50e+03 pdb=" O AARG B 293 " -0.038 2.00e-02 2.50e+03 pdb=" N ALA B 294 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 31 " 0.020 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" CG ASP A 31 " -0.072 2.00e-02 2.50e+03 pdb=" OD1 ASP A 31 " 0.026 2.00e-02 2.50e+03 pdb=" OD2 ASP A 31 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 31 " 0.020 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" CG ASP B 31 " -0.072 2.00e-02 2.50e+03 pdb=" OD1 ASP B 31 " 0.026 2.00e-02 2.50e+03 pdb=" OD2 ASP B 31 " 0.026 2.00e-02 2.50e+03 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1500 2.75 - 3.29: 12715 3.29 - 3.83: 22221 3.83 - 4.36: 29594 4.36 - 4.90: 50622 Nonbonded interactions: 116652 Sorted by model distance: nonbonded pdb=" OH TYR D 254 " pdb=" O HOH D 501 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR A 254 " pdb=" O HOH A 501 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR E 254 " pdb=" O HOH E 501 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR C 254 " pdb=" O HOH C 501 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR B 254 " pdb=" O HOH B 501 " model vdw 2.214 3.040 ... (remaining 116647 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 292 or resid 294 through 316 or (resid 403 throu \ gh 404 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 C18 or name C2 or name C3 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name O1P or name O2 or name O2P or name O3 or name O3P or n \ ame O4 or name O4P or name O5 or name P )) 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 nam \ e C30 or name C31 or name C32 or name C33 or name C4 or name C5 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or (resid 407 and (name N or 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 C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or n \ ame 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 O2P \ or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid \ 408 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 o \ r name C20 or name C21 or name C22 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 C39 or name C4 or name C40 or name C5 or name O1P or name O2 or name O2P or na \ me O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 409 t \ hrough 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 throu \ gh 404 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 C18 or name C2 or name C3 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name O1P or name O2 or name O2P or name O3 or name O3P or n \ ame O4 or name O4P or name O5 or name P )) 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 nam \ e C30 or name C31 or name C32 or name C33 or name C4 or name C5 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or (resid 407 and (name N or 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 C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or n \ ame 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 O2P \ or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid \ 408 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 o \ r name C20 or name C21 or name C22 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 C39 or name C4 or name C40 or name C5 or name O1P or name O2 or name O2P or na \ me O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 409 t \ hrough 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 throu \ gh 404 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 C18 or name C2 or name C3 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name O1P or name O2 or name O2P or name O3 or name O3P or n \ ame O4 or name O4P or name O5 or name P )) 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 nam \ e C30 or name C31 or name C32 or name C33 or name C4 or name C5 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or (resid 407 and (name N or 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 C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or n \ ame 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 O2P \ or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid \ 408 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 o \ r name C20 or name C21 or name C22 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 C39 or name C4 or name C40 or name C5 or name O1P or name O2 or name O2P or na \ me O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 409 t \ hrough 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 throu \ gh 404 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 C18 or name C2 or name C3 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name O1P or name O2 or name O2P or name O3 or name O3P or n \ ame O4 or name O4P or name O5 or name P )) 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 nam \ e C30 or name C31 or name C32 or name C33 or name C4 or name C5 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or (resid 407 and (name N or 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 C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or n \ ame 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 O2P \ or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid \ 408 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 o \ r name C20 or name C21 or name C22 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 C39 or name C4 or name C40 or name C5 or name O1P or name O2 or name O2P or na \ me O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 409 t \ hrough 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 throu \ gh 404 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 C18 or name C2 or name C3 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name O1P or name O2 or name O2P or name O3 or name O3P or n \ ame O4 or name O4P or name O5 or name P )) 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 nam \ e C30 or name C31 or name C32 or name C33 or name C4 or name C5 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or (resid 407 and (name N or 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 C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 or n \ ame 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 O2P \ or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid \ 408 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 o \ r name C20 or name C21 or name C22 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 C39 or name C4 or name C40 or name C5 or name O1P or name O2 or name O2P or na \ me O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 409 t \ hrough 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=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.080 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 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 0.067 14665 Z= 0.232 Angle : 0.882 10.243 19650 Z= 0.451 Chirality : 0.064 0.629 2120 Planarity : 0.011 0.079 2320 Dihedral : 26.739 161.818 6110 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.14 % Allowed : 20.57 % Favored : 77.30 % 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: -0.45 (0.19), residues: 1565 helix: 0.82 (0.19), residues: 510 sheet: -0.28 (0.25), residues: 385 loop : -1.13 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.005 ARG A 50 TYR 0.051 0.009 TYR D 278 PHE 0.035 0.006 PHE B 265 TRP 0.054 0.009 TRP E 213 HIS 0.032 0.008 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00502 (14665) covalent geometry : angle 0.88229 (19650) hydrogen bonds : bond 0.18089 ( 625) hydrogen bonds : angle 6.52618 ( 2210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.456 Fit side-chains REVERT: D 50 ARG cc_start: 0.8427 (tpp80) cc_final: 0.8046 (mpt-90) outliers start: 25 outliers final: 21 residues processed: 117 average time/residue: 0.6489 time to fit residues: 82.2347 Evaluate side-chains 110 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 83 ASN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E 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: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 139 ASN C 139 ASN B 139 ASN D 139 ASN D 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.092372 restraints weight = 47980.687| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.14 r_work: 0.2858 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14665 Z= 0.186 Angle : 0.635 7.601 19650 Z= 0.325 Chirality : 0.046 0.150 2120 Planarity : 0.005 0.039 2320 Dihedral : 28.169 157.035 3188 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.14 % Allowed : 19.79 % Favored : 78.08 % 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: 0.79 (0.20), residues: 1565 helix: 2.46 (0.20), residues: 545 sheet: 0.02 (0.24), residues: 385 loop : -0.87 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 105 TYR 0.016 0.002 TYR C 102 PHE 0.014 0.002 PHE A 210 TRP 0.011 0.001 TRP A 47 HIS 0.005 0.002 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00440 (14665) covalent geometry : angle 0.63452 (19650) hydrogen bonds : bond 0.08460 ( 625) hydrogen bonds : angle 4.42483 ( 2210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.533 Fit side-chains outliers start: 25 outliers final: 24 residues processed: 145 average time/residue: 0.7055 time to fit residues: 110.3831 Evaluate side-chains 130 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 219 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 10 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN C 101 GLN E 101 GLN E 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.138931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.095767 restraints weight = 50081.921| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.27 r_work: 0.2912 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14665 Z= 0.133 Angle : 0.558 7.064 19650 Z= 0.283 Chirality : 0.043 0.145 2120 Planarity : 0.004 0.034 2320 Dihedral : 26.288 153.889 3183 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.28 % Allowed : 19.64 % Favored : 78.08 % 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 (0.20), residues: 1565 helix: 2.94 (0.20), residues: 545 sheet: 0.25 (0.25), residues: 385 loop : -0.77 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 179 TYR 0.011 0.001 TYR D 102 PHE 0.007 0.001 PHE D 37 TRP 0.007 0.001 TRP E 47 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00299 (14665) covalent geometry : angle 0.55849 (19650) hydrogen bonds : bond 0.06668 ( 625) hydrogen bonds : angle 4.02728 ( 2210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.437 Fit side-chains REVERT: E 282 GLU cc_start: 0.6688 (tt0) cc_final: 0.6384 (tt0) outliers start: 27 outliers final: 20 residues processed: 155 average time/residue: 0.6856 time to fit residues: 115.0182 Evaluate side-chains 149 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 137 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 47 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.133169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.089857 restraints weight = 46470.118| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.13 r_work: 0.2804 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 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 = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 14665 Z= 0.226 Angle : 0.664 7.942 19650 Z= 0.338 Chirality : 0.047 0.159 2120 Planarity : 0.005 0.038 2320 Dihedral : 26.588 158.175 3179 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.99 % Allowed : 20.14 % Favored : 76.87 % 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: 1.01 (0.20), residues: 1565 helix: 2.59 (0.20), residues: 545 sheet: 0.31 (0.25), residues: 385 loop : -0.82 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 179 TYR 0.009 0.002 TYR D 23 PHE 0.013 0.002 PHE A 210 TRP 0.008 0.001 TRP D 213 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00553 (14665) covalent geometry : angle 0.66417 (19650) hydrogen bonds : bond 0.09528 ( 625) hydrogen bonds : angle 4.27921 ( 2210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.519 Fit side-chains REVERT: A 48 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.7665 (ttmt) REVERT: A 101 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7783 (mm-40) REVERT: C 48 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.7826 (ttmt) REVERT: B 139 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7874 (t0) REVERT: E 282 GLU cc_start: 0.7212 (tt0) cc_final: 0.6898 (tt0) outliers start: 37 outliers final: 25 residues processed: 154 average time/residue: 0.6937 time to fit residues: 115.6488 Evaluate side-chains 156 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 169 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 118 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 146 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.140420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.096770 restraints weight = 62470.881| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.58 r_work: 0.2964 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14665 Z= 0.111 Angle : 0.536 6.745 19650 Z= 0.271 Chirality : 0.043 0.140 2120 Planarity : 0.004 0.036 2320 Dihedral : 24.704 152.862 3179 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.14 % Allowed : 21.21 % Favored : 76.65 % 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: 1.40 (0.20), residues: 1565 helix: 3.12 (0.20), residues: 540 sheet: 0.52 (0.25), residues: 385 loop : -0.78 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 117 TYR 0.012 0.001 TYR C 102 PHE 0.009 0.001 PHE A 156 TRP 0.007 0.001 TRP E 47 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00235 (14665) covalent geometry : angle 0.53634 (19650) hydrogen bonds : bond 0.05649 ( 625) hydrogen bonds : angle 3.83471 ( 2210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.434 Fit side-chains REVERT: B 101 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7684 (mm-40) REVERT: D 252 MET cc_start: 0.8625 (tpt) cc_final: 0.8394 (tpt) REVERT: E 282 GLU cc_start: 0.6389 (tt0) cc_final: 0.6103 (tt0) outliers start: 25 outliers final: 16 residues processed: 158 average time/residue: 0.6519 time to fit residues: 111.9126 Evaluate side-chains 151 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 112 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN D 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.137112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.094153 restraints weight = 44395.270| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.08 r_work: 0.2865 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14665 Z= 0.152 Angle : 0.582 7.118 19650 Z= 0.294 Chirality : 0.044 0.150 2120 Planarity : 0.004 0.038 2320 Dihedral : 23.939 155.517 3173 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.63 % Allowed : 20.93 % Favored : 76.44 % 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: 1.31 (0.20), residues: 1565 helix: 2.90 (0.20), residues: 545 sheet: 0.51 (0.25), residues: 385 loop : -0.75 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 179 TYR 0.010 0.001 TYR C 102 PHE 0.014 0.001 PHE D 156 TRP 0.005 0.001 TRP D 47 HIS 0.002 0.001 HIS C 127 Details of bonding type rmsd covalent geometry : bond 0.00352 (14665) covalent geometry : angle 0.58234 (19650) hydrogen bonds : bond 0.07528 ( 625) hydrogen bonds : angle 3.94200 ( 2210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.482 Fit side-chains REVERT: B 101 GLN cc_start: 0.8379 (mm-40) cc_final: 0.7776 (mm-40) REVERT: E 205 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7202 (mmp) REVERT: E 282 GLU cc_start: 0.6931 (tt0) cc_final: 0.6610 (tt0) outliers start: 32 outliers final: 23 residues processed: 152 average time/residue: 0.6565 time to fit residues: 108.2432 Evaluate side-chains 160 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 205 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 127 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN B 139 ASN D 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.133152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.089031 restraints weight = 54953.688| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.37 r_work: 0.2794 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 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 = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14665 Z= 0.213 Angle : 0.645 7.860 19650 Z= 0.330 Chirality : 0.046 0.161 2120 Planarity : 0.005 0.041 2320 Dihedral : 23.828 160.935 3173 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.20 % Allowed : 19.93 % Favored : 76.87 % 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: 1.09 (0.20), residues: 1565 helix: 2.62 (0.20), residues: 545 sheet: 0.49 (0.25), residues: 385 loop : -0.85 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 58 TYR 0.010 0.002 TYR D 66 PHE 0.015 0.002 PHE D 156 TRP 0.008 0.001 TRP D 213 HIS 0.003 0.001 HIS C 127 Details of bonding type rmsd covalent geometry : bond 0.00516 (14665) covalent geometry : angle 0.64471 (19650) hydrogen bonds : bond 0.09358 ( 625) hydrogen bonds : angle 4.18269 ( 2210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.450 Fit side-chains REVERT: A 48 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7676 (ttmt) REVERT: C 48 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.7802 (ttmt) REVERT: B 205 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7783 (mmp) REVERT: E 205 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7305 (mmp) outliers start: 40 outliers final: 27 residues processed: 156 average time/residue: 0.7143 time to fit residues: 120.6187 Evaluate side-chains 158 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 205 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 32 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN B 139 ASN D 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.093515 restraints weight = 45266.967| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.10 r_work: 0.2912 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14665 Z= 0.163 Angle : 0.587 7.431 19650 Z= 0.301 Chirality : 0.045 0.155 2120 Planarity : 0.004 0.041 2320 Dihedral : 23.040 159.459 3173 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.85 % Allowed : 20.14 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.20), residues: 1565 helix: 2.81 (0.20), residues: 545 sheet: 0.55 (0.25), residues: 385 loop : -0.84 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 58 TYR 0.011 0.001 TYR C 102 PHE 0.013 0.001 PHE D 156 TRP 0.005 0.001 TRP E 213 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00383 (14665) covalent geometry : angle 0.58682 (19650) hydrogen bonds : bond 0.07905 ( 625) hydrogen bonds : angle 4.04248 ( 2210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.575 Fit side-chains REVERT: A 48 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7659 (ttmt) REVERT: C 48 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.7798 (ttmt) REVERT: B 101 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7740 (mm-40) outliers start: 35 outliers final: 26 residues processed: 161 average time/residue: 0.6998 time to fit residues: 122.1684 Evaluate side-chains 158 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 169 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 124 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN B 139 ASN D 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.134475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.091089 restraints weight = 45090.016| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.11 r_work: 0.2854 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 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 = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14665 Z= 0.177 Angle : 0.601 7.448 19650 Z= 0.309 Chirality : 0.045 0.155 2120 Planarity : 0.004 0.041 2320 Dihedral : 22.921 162.290 3173 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.63 % Allowed : 20.28 % Favored : 77.08 % 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: 1.18 (0.20), residues: 1565 helix: 2.75 (0.20), residues: 545 sheet: 0.55 (0.25), residues: 385 loop : -0.86 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 58 TYR 0.010 0.001 TYR C 102 PHE 0.013 0.002 PHE D 37 TRP 0.006 0.001 TRP D 213 HIS 0.002 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00421 (14665) covalent geometry : angle 0.60101 (19650) hydrogen bonds : bond 0.08373 ( 625) hydrogen bonds : angle 4.07697 ( 2210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.545 Fit side-chains REVERT: A 48 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7660 (ttmt) REVERT: C 48 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7790 (ttmt) REVERT: B 101 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7750 (mm-40) outliers start: 32 outliers final: 27 residues processed: 147 average time/residue: 0.7430 time to fit residues: 118.1921 Evaluate side-chains 157 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 30 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN B 139 ASN D 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.133459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.090069 restraints weight = 42678.484| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.05 r_work: 0.2821 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14665 Z= 0.207 Angle : 0.636 7.931 19650 Z= 0.328 Chirality : 0.046 0.160 2120 Planarity : 0.005 0.043 2320 Dihedral : 23.349 166.955 3173 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.78 % Allowed : 20.14 % Favored : 77.08 % 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: 1.08 (0.20), residues: 1565 helix: 2.62 (0.20), residues: 545 sheet: 0.54 (0.25), residues: 385 loop : -0.89 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 58 TYR 0.009 0.002 TYR B 66 PHE 0.014 0.002 PHE D 37 TRP 0.008 0.001 TRP D 213 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00502 (14665) covalent geometry : angle 0.63643 (19650) hydrogen bonds : bond 0.09193 ( 625) hydrogen bonds : angle 4.18640 ( 2210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.438 Fit side-chains REVERT: A 48 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7707 (ttmt) REVERT: C 48 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7831 (ttmt) REVERT: B 101 GLN cc_start: 0.8467 (mm-40) cc_final: 0.7819 (mm-40) outliers start: 34 outliers final: 27 residues processed: 148 average time/residue: 0.7000 time to fit residues: 112.0790 Evaluate side-chains 154 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 120 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN C 139 ASN B 139 ASN D 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.137737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.094004 restraints weight = 53869.576| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.37 r_work: 0.2919 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14665 Z= 0.141 Angle : 0.561 7.310 19650 Z= 0.289 Chirality : 0.044 0.149 2120 Planarity : 0.004 0.041 2320 Dihedral : 22.412 165.396 3173 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.42 % Allowed : 20.50 % Favored : 77.08 % 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 (0.20), residues: 1565 helix: 2.91 (0.20), residues: 545 sheet: 0.61 (0.25), residues: 385 loop : -0.82 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 105 TYR 0.011 0.001 TYR C 102 PHE 0.013 0.001 PHE D 156 TRP 0.005 0.001 TRP D 47 HIS 0.002 0.001 HIS E 127 Details of bonding type rmsd covalent geometry : bond 0.00318 (14665) covalent geometry : angle 0.56088 (19650) hydrogen bonds : bond 0.07123 ( 625) hydrogen bonds : angle 3.95410 ( 2210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4583.52 seconds wall clock time: 78 minutes 36.89 seconds (4716.89 seconds total)