Starting phenix.real_space_refine on Fri Jul 3 13:58:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jj3_36339/07_2026/8jj3_36339.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jj3_36339/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jj3_36339/07_2026/8jj3_36339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jj3_36339/07_2026/8jj3_36339.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jj3_36339/07_2026/8jj3_36339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jj3_36339/07_2026/8jj3_36339.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 333 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 1 Unresolved non-hydrogen bonds: 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, 333 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 1 Unresolved non-hydrogen bonds: 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, 333 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 9} Classifications: {'undetermined': 9} Link IDs: {None: 7} Chain breaks: 1 Unresolved non-hydrogen bonds: 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, 333 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 9} Classifications: {'undetermined': 9} Link IDs: {None: 7} Chain breaks: 1 Unresolved non-hydrogen bonds: 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, 333 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 9} Classifications: {'undetermined': 9} Link IDs: {None: 7} Chain breaks: 1 Unresolved non-hydrogen bonds: 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: 4.90, per 1000 atoms: 0.33 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: 1.10 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.59 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: 2.73 Time building geometry restraints manager: 1.51 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: 1.480 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.890 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 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/Z covalent geometry : bond 0.00502 / 0.23 (14665) covalent geometry : angle 0.88229 / 0.45 (19650) hydrogen bonds : bond 0.18089 / 12.08 ( 625) hydrogen bonds : angle 6.52618 / 4.49 ( 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 : 0.467 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: 0.6035 time to fit residues: 76.7674 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 : 0.547 ------------------------------------------------------------------------------- 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... A 101 GLN A 139 ASN C 139 ASN B 139 ASN D 139 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.092381 restraints weight = 47979.146| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.14 r_work: 0.2858 rms_B_bonded: 4.00 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1039 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 : 28.168 157.035 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 : 2.06 % Allowed : 19.86 % 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/Z covalent geometry : bond 0.00440 / 0.19 (14665) covalent geometry : angle 0.63452 / 0.33 (19650) hydrogen bonds : bond 0.08460 / 5.74 ( 625) hydrogen bonds : angle 4.42490 / 3.02 ( 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 146 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.490 Fit side-chains outliers start: 24 outliers final: 23 residues processed: 144 average time/residue: 0.7110 time to fit residues: 110.9151 Evaluate side-chains 129 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 79 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN C 101 GLN E 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.093093 restraints weight = 48410.484| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.18 r_work: 0.2851 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 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 = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1367 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= 0.168 Angle : 0.603 7.451 19650 Z= 0.307 Chirality : 0.045 0.153 2120 Planarity : 0.005 0.035 2320 Dihedral : 26.781 155.624 3182 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.56 % Allowed : 19.86 % Favored : 77.58 % 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: 1.07 (0.20), residues: 1565 helix: 2.84 (0.20), residues: 540 sheet: 0.24 (0.25), residues: 385 loop : -0.90 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 105 TYR 0.010 0.001 TYR C 102 PHE 0.010 0.001 PHE C 195 TRP 0.007 0.001 TRP E 47 HIS 0.002 0.001 HIS E 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (14665) covalent geometry : angle 0.60271 / 0.31 (19650) hydrogen bonds : bond 0.08066 / 5.46 ( 625) hydrogen bonds : angle 4.18750 / 2.86 ( 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 172 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.515 Fit side-chains REVERT: B 101 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7738 (mm-40) REVERT: E 282 GLU cc_start: 0.7020 (tt0) cc_final: 0.6707 (tt0) outliers start: 31 outliers final: 22 residues processed: 160 average time/residue: 0.6646 time to fit residues: 115.4943 Evaluate side-chains 151 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 47 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN E 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.088838 restraints weight = 46328.033| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.14 r_work: 0.2793 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 14665 Z= 0.240 Angle : 0.684 8.100 19650 Z= 0.348 Chirality : 0.047 0.163 2120 Planarity : 0.005 0.041 2320 Dihedral : 26.921 159.791 3179 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.20 % Allowed : 20.21 % Favored : 76.58 % 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: 0.95 (0.20), residues: 1565 helix: 2.51 (0.20), residues: 545 sheet: 0.33 (0.25), residues: 385 loop : -0.87 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 118 TYR 0.010 0.002 TYR D 266 PHE 0.013 0.002 PHE A 210 TRP 0.009 0.001 TRP D 213 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.24 (14665) covalent geometry : angle 0.68369 / 0.35 (19650) hydrogen bonds : bond 0.09853 / 6.69 ( 625) hydrogen bonds : angle 4.35018 / 2.97 ( 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 169 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.332 Fit side-chains REVERT: A 48 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7672 (ttmt) REVERT: C 48 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.7820 (ttmt) REVERT: E 48 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8421 (ttmt) REVERT: E 179 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6628 (mmt-90) outliers start: 40 outliers final: 28 residues processed: 152 average time/residue: 0.6419 time to fit residues: 105.8960 Evaluate side-chains 154 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 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 219 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 48 LYS 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 179 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 118 optimal weight: 0.9980 chunk 130 optimal weight: 0.0670 chunk 121 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 146 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3671 r_free = 0.3671 target = 0.139661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.095815 restraints weight = 62153.632| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.58 r_work: 0.2947 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14665 Z= 0.114 Angle : 0.545 6.954 19650 Z= 0.276 Chirality : 0.043 0.143 2120 Planarity : 0.004 0.038 2320 Dihedral : 25.040 154.541 3179 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.56 % Allowed : 20.64 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.20), residues: 1565 helix: 3.11 (0.20), residues: 540 sheet: 0.53 (0.25), residues: 385 loop : -0.83 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 192 TYR 0.012 0.001 TYR D 102 PHE 0.008 0.001 PHE C 156 TRP 0.005 0.001 TRP E 47 HIS 0.001 0.001 HIS D 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (14665) covalent geometry : angle 0.54527 / 0.28 (19650) hydrogen bonds : bond 0.06001 / 4.06 ( 625) hydrogen bonds : angle 3.91325 / 2.66 ( 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 172 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.555 Fit side-chains REVERT: B 101 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7686 (mm-40) REVERT: E 282 GLU cc_start: 0.6583 (tt0) cc_final: 0.6101 (tt0) outliers start: 31 outliers final: 21 residues processed: 161 average time/residue: 0.6080 time to fit residues: 106.5676 Evaluate side-chains 157 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 191 SER 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 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 219 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3648 r_free = 0.3648 target = 0.137696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.094586 restraints weight = 44774.153| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.11 r_work: 0.2937 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14665 Z= 0.141 Angle : 0.574 7.016 19650 Z= 0.290 Chirality : 0.044 0.149 2120 Planarity : 0.004 0.040 2320 Dihedral : 23.763 156.486 3176 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.70 % Allowed : 20.78 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.20), residues: 1565 helix: 2.97 (0.20), residues: 545 sheet: 0.56 (0.26), residues: 385 loop : -0.75 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 133 TYR 0.011 0.001 TYR C 102 PHE 0.018 0.001 PHE A 156 TRP 0.005 0.001 TRP D 47 HIS 0.002 0.001 HIS E 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (14665) covalent geometry : angle 0.57403 / 0.29 (19650) hydrogen bonds : bond 0.07202 / 4.88 ( 625) hydrogen bonds : angle 3.92339 / 2.68 ( 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 168 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.384 Fit side-chains REVERT: A 48 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7673 (ttmt) REVERT: C 48 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7804 (ttmt) REVERT: B 101 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7728 (mm-40) REVERT: E 205 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7137 (mmp) REVERT: E 282 GLU cc_start: 0.6827 (tt0) cc_final: 0.6430 (tt0) outliers start: 33 outliers final: 26 residues processed: 157 average time/residue: 0.6231 time to fit residues: 106.3041 Evaluate side-chains 164 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 A residue 191 SER 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 169 VAL Chi-restraints excluded: chain C residue 191 SER 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 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 169 VAL Chi-restraints excluded: chain D residue 219 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 139 ASN 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: 0.7980 chunk 64 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3624 r_free = 0.3624 target = 0.135772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.091474 restraints weight = 55609.706| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.40 r_work: 0.2809 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 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 = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14665 Z= 0.176 Angle : 0.601 7.374 19650 Z= 0.309 Chirality : 0.045 0.154 2120 Planarity : 0.004 0.042 2320 Dihedral : 23.217 160.296 3174 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.35 % Allowed : 19.79 % 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: 1.23 (0.20), residues: 1565 helix: 2.80 (0.20), residues: 545 sheet: 0.55 (0.25), residues: 385 loop : -0.83 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 58 TYR 0.010 0.001 TYR C 102 PHE 0.016 0.002 PHE A 156 TRP 0.006 0.001 TRP D 213 HIS 0.002 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (14665) covalent geometry : angle 0.60109 / 0.31 (19650) hydrogen bonds : bond 0.08429 / 5.72 ( 625) hydrogen bonds : angle 4.08252 / 2.79 ( 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 176 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.556 Fit side-chains REVERT: A 48 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.7714 (ttmt) REVERT: C 48 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7852 (ttmt) REVERT: E 48 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8473 (ttmt) REVERT: E 205 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7320 (mmp) outliers start: 42 outliers final: 27 residues processed: 159 average time/residue: 0.6440 time to fit residues: 111.6183 Evaluate side-chains 160 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 219 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 48 LYS 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: 5.9990 chunk 112 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3633 r_free = 0.3633 target = 0.136468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.093431 restraints weight = 45360.455| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.10 r_work: 0.2850 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 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 = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1726 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= 0.164 Angle : 0.586 7.252 19650 Z= 0.301 Chirality : 0.045 0.153 2120 Planarity : 0.004 0.042 2320 Dihedral : 22.762 160.923 3174 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.99 % Allowed : 20.00 % 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: 1.26 (0.20), residues: 1565 helix: 2.85 (0.20), residues: 545 sheet: 0.57 (0.25), residues: 385 loop : -0.83 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 58 TYR 0.011 0.001 TYR C 102 PHE 0.016 0.001 PHE A 156 TRP 0.005 0.001 TRP D 213 HIS 0.002 0.001 HIS E 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (14665) covalent geometry : angle 0.58598 / 0.30 (19650) hydrogen bonds : bond 0.07885 / 5.34 ( 625) hydrogen bonds : angle 4.02079 / 2.74 ( 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 173 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.578 Fit side-chains REVERT: A 48 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7648 (ttmt) REVERT: C 48 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.7777 (ttmt) REVERT: B 101 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7778 (mm-40) REVERT: E 48 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8422 (ttmt) outliers start: 37 outliers final: 27 residues processed: 158 average time/residue: 0.6386 time to fit residues: 110.0610 Evaluate side-chains 161 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 219 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 48 LYS 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=1.50 ------------------------------------------------------------------------------- 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: 0.0970 chunk 50 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3604 r_free = 0.3604 target = 0.133768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.090373 restraints weight = 45010.129| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.10 r_work: 0.2822 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14665 Z= 0.198 Angle : 0.622 7.698 19650 Z= 0.320 Chirality : 0.046 0.157 2120 Planarity : 0.005 0.043 2320 Dihedral : 23.075 164.669 3174 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: 1.15 (0.20), residues: 1565 helix: 2.71 (0.20), residues: 545 sheet: 0.56 (0.25), residues: 385 loop : -0.87 (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 A 156 TRP 0.007 0.001 TRP D 213 HIS 0.003 0.001 HIS E 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (14665) covalent geometry : angle 0.62240 / 0.32 (19650) hydrogen bonds : bond 0.08886 / 6.03 ( 625) hydrogen bonds : angle 4.12915 / 2.82 ( 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 : 0.539 Fit side-chains REVERT: A 48 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.7677 (ttmt) REVERT: C 48 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.7803 (ttmt) REVERT: B 101 GLN cc_start: 0.8402 (mm-40) cc_final: 0.7782 (mm-40) REVERT: E 48 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8445 (ttmt) outliers start: 32 outliers final: 26 residues processed: 148 average time/residue: 0.7008 time to fit residues: 112.6943 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 : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 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 219 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 48 LYS 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 30 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3611 r_free = 0.3611 target = 0.134327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.091198 restraints weight = 42836.761| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.03 r_work: 0.2830 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14665 Z= 0.187 Angle : 0.608 7.545 19650 Z= 0.313 Chirality : 0.045 0.156 2120 Planarity : 0.005 0.043 2320 Dihedral : 22.977 166.796 3174 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.85 % Allowed : 19.86 % 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: 1.19 (0.20), residues: 1565 helix: 2.75 (0.20), residues: 545 sheet: 0.59 (0.25), 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 0.011 0.002 TYR C 102 PHE 0.015 0.002 PHE A 156 TRP 0.006 0.001 TRP D 213 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (14665) covalent geometry : angle 0.60810 / 0.31 (19650) hydrogen bonds : bond 0.08423 / 5.71 ( 625) hydrogen bonds : angle 4.09427 / 2.79 ( 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: 35 poor density : 126 time to evaluate : 0.470 Fit side-chains REVERT: A 48 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7696 (ttmt) REVERT: C 48 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.7828 (ttmt) REVERT: B 101 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7786 (mm-40) REVERT: E 48 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8475 (ttmt) REVERT: E 205 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7218 (mmp) outliers start: 35 outliers final: 27 residues processed: 147 average time/residue: 0.6702 time to fit residues: 106.9857 Evaluate side-chains 156 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 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 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 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 219 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 48 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 120 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3657 r_free = 0.3657 target = 0.138558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.094757 restraints weight = 53953.703| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.38 r_work: 0.2929 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14665 Z= 0.126 Angle : 0.543 7.206 19650 Z= 0.280 Chirality : 0.043 0.145 2120 Planarity : 0.004 0.041 2320 Dihedral : 22.066 166.598 3174 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.56 % Allowed : 20.00 % Favored : 77.44 % 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: 1.42 (0.20), residues: 1565 helix: 3.02 (0.20), residues: 545 sheet: 0.67 (0.25), residues: 385 loop : -0.78 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 189 TYR 0.012 0.001 TYR C 102 PHE 0.014 0.001 PHE A 156 TRP 0.005 0.001 TRP D 47 HIS 0.002 0.001 HIS E 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (14665) covalent geometry : angle 0.54297 / 0.28 (19650) hydrogen bonds : bond 0.06621 / 4.48 ( 625) hydrogen bonds : angle 3.89044 / 2.65 ( 2210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4560.66 seconds wall clock time: 78 minutes 28.09 seconds (4708.09 seconds total)