Starting phenix.real_space_refine on Sat Oct 11 10:52:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcq_37446/10_2025/8wcq_37446.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcq_37446/10_2025/8wcq_37446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wcq_37446/10_2025/8wcq_37446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcq_37446/10_2025/8wcq_37446.map" model { file = "/net/cci-nas-00/data/ceres_data/8wcq_37446/10_2025/8wcq_37446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcq_37446/10_2025/8wcq_37446.cif" } resolution = 3.35 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 35 5.49 5 S 20 5.16 5 Cl 5 4.86 5 C 9455 2.51 5 N 2065 2.21 5 O 2550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14130 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "E" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "B" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "C" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "D" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "A" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 289 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 122 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: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 289 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 122 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: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 289 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 122 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: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 289 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 122 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: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 289 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 5.90, per 1000 atoms: 0.42 Number of scatterers: 14130 At special positions: 0 Unit cell: (92.72, 92.72, 125.4, 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 35 15.00 O 2550 8.00 N 2065 7.00 C 9455 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: 1.31 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 20 sheets defined 38.1% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 50 through 53 Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.756A pdb=" N TYR A 197 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 213 removed outlier: 3.596A pdb=" N MET A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.710A pdb=" N SER A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) 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 315 removed outlier: 3.519A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'E' and resid 50 through 53 Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 194 through 198 removed outlier: 3.757A pdb=" N TYR E 197 " --> pdb=" O TYR E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 213 removed outlier: 3.595A pdb=" N MET E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 218 removed outlier: 3.711A pdb=" N SER E 218 " --> pdb=" O ALA E 215 " (cutoff:3.500A) 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 315 removed outlier: 3.520A pdb=" N ALA E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing helix chain 'B' and resid 50 through 53 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.757A pdb=" N TYR B 197 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 213 removed outlier: 3.595A pdb=" N MET B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 218 removed outlier: 3.711A pdb=" N SER B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) 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 315 removed outlier: 3.520A pdb=" N ALA B 288 " --> pdb=" O GLN B 284 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'C' and resid 50 through 53 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 194 through 198 removed outlier: 3.756A pdb=" N TYR C 197 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 213 removed outlier: 3.595A pdb=" N MET C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 218 removed outlier: 3.711A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) 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 315 removed outlier: 3.521A pdb=" N ALA C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 50 through 53 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 194 through 198 removed outlier: 3.756A pdb=" N TYR D 197 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 213 removed outlier: 3.595A pdb=" N MET D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 218 removed outlier: 3.710A pdb=" N SER D 218 " --> pdb=" O ALA D 215 " (cutoff:3.500A) 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 315 removed outlier: 3.520A pdb=" N ALA D 288 " --> pdb=" O GLN D 284 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 removed outlier: 5.948A pdb=" N LEU A 16 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA A 143 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 18 " --> pdb=" O ALA A 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 94 removed outlier: 5.231A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 108 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS A 38 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N SER A 29 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN A 40 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N CYS A 27 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N PHE A 42 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE A 25 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N SER A 44 " --> pdb=" O TYR A 23 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N TYR A 23 " --> pdb=" O SER A 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 78 removed outlier: 4.370A pdb=" N ASP A 185 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 164 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER A 191 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE A 162 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'E' and resid 16 through 20 removed outlier: 5.947A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 88 through 94 removed outlier: 5.230A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA E 108 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS E 38 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER E 29 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN E 40 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N CYS E 27 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N PHE E 42 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE E 25 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N SER E 44 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N TYR E 23 " --> pdb=" O SER E 44 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 78 removed outlier: 4.369A pdb=" N ASP E 185 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER E 164 " --> pdb=" O ARG E 189 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER E 191 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE E 162 " --> pdb=" O SER E 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'B' and resid 16 through 20 removed outlier: 5.947A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA B 143 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 88 through 94 removed outlier: 5.231A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 108 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS B 38 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER B 29 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASN B 40 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N CYS B 27 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N PHE B 42 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE B 25 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N SER B 44 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N TYR B 23 " --> pdb=" O SER B 44 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 77 through 78 removed outlier: 4.370A pdb=" N ASP B 185 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 164 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER B 191 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE B 162 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AB4, first strand: chain 'C' and resid 16 through 20 removed outlier: 5.948A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 88 through 94 removed outlier: 5.231A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 108 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS C 38 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER C 29 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN C 40 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N CYS C 27 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N PHE C 42 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE C 25 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N SER C 44 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N TYR C 23 " --> pdb=" O SER C 44 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 77 through 78 removed outlier: 4.370A pdb=" N ASP C 185 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER C 164 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER C 191 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE C 162 " --> pdb=" O SER C 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB8, first strand: chain 'D' and resid 16 through 20 removed outlier: 5.948A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA D 143 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL D 18 " --> pdb=" O ALA D 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 88 through 94 removed outlier: 5.231A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 108 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS D 38 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER D 29 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN D 40 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N CYS D 27 " --> pdb=" O ASN D 40 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N PHE D 42 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE D 25 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N SER D 44 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N TYR D 23 " --> pdb=" O SER D 44 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 77 through 78 removed outlier: 4.370A pdb=" N ASP D 185 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER D 164 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER D 191 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE D 162 " --> pdb=" O SER D 191 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 77 through 78 655 hydrogen bonds defined for protein. 1840 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: 2.35 Time building geometry restraints manager: 1.64 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: 2182 1.32 - 1.44: 3753 1.44 - 1.57: 8390 1.57 - 1.69: 70 1.69 - 1.81: 35 Bond restraints: 14430 Sorted by residual: bond pdb=" CB AARG A 293 " pdb=" CG AARG A 293 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.42e+00 bond pdb=" CB AARG B 293 " pdb=" CG AARG B 293 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.42e+00 bond pdb=" CB AARG E 293 " pdb=" CG AARG E 293 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.34e+00 bond pdb=" CB AARG C 293 " pdb=" CG AARG C 293 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.34e+00 bond pdb=" CB AARG D 293 " pdb=" CG AARG D 293 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.33e+00 ... (remaining 14425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 18571 1.08 - 2.16: 624 2.16 - 3.24: 140 3.24 - 4.32: 30 4.32 - 5.40: 20 Bond angle restraints: 19385 Sorted by residual: angle pdb=" CA LYS C 248 " pdb=" CB LYS C 248 " pdb=" CG LYS C 248 " ideal model delta sigma weight residual 114.10 119.25 -5.15 2.00e+00 2.50e-01 6.62e+00 angle pdb=" CA LYS A 248 " pdb=" CB LYS A 248 " pdb=" CG LYS A 248 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" CA LYS E 248 " pdb=" CB LYS E 248 " pdb=" CG LYS E 248 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" CA LYS B 248 " pdb=" CB LYS B 248 " pdb=" CG LYS B 248 " ideal model delta sigma weight residual 114.10 119.23 -5.13 2.00e+00 2.50e-01 6.58e+00 angle pdb=" CA LYS D 248 " pdb=" CB LYS D 248 " pdb=" CG LYS D 248 " ideal model delta sigma weight residual 114.10 119.20 -5.10 2.00e+00 2.50e-01 6.50e+00 ... (remaining 19380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 8599 34.73 - 69.46: 256 69.46 - 104.18: 60 104.18 - 138.91: 35 138.91 - 173.64: 20 Dihedral angle restraints: 8970 sinusoidal: 4270 harmonic: 4700 Sorted by residual: dihedral pdb=" C4 PEE D 401 " pdb=" O4P PEE D 401 " pdb=" P PEE D 401 " pdb=" O1P PEE D 401 " ideal model delta sinusoidal sigma weight residual 57.28 -129.08 -173.64 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C4 PEE B 401 " pdb=" O4P PEE B 401 " pdb=" P PEE B 401 " pdb=" O1P PEE B 401 " ideal model delta sinusoidal sigma weight residual 57.28 -129.11 -173.61 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C4 PEE E 409 " pdb=" O4P PEE E 409 " pdb=" P PEE E 409 " pdb=" O1P PEE E 409 " ideal model delta sinusoidal sigma weight residual 57.28 -129.13 -173.59 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1211 0.028 - 0.055: 501 0.055 - 0.083: 215 0.083 - 0.111: 148 0.111 - 0.139: 40 Chirality restraints: 2115 Sorted by residual: chirality pdb=" CA ILE D 92 " pdb=" N ILE D 92 " pdb=" C ILE D 92 " pdb=" CB ILE D 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE B 92 " pdb=" N ILE B 92 " pdb=" C ILE B 92 " pdb=" CB ILE B 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE E 92 " pdb=" N ILE E 92 " pdb=" C ILE E 92 " pdb=" CB ILE E 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 2112 not shown) Planarity restraints: 2305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 246 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO A 247 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 246 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO D 247 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 247 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 247 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 246 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.79e+00 pdb=" N PRO B 247 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " -0.033 5.00e-02 4.00e+02 ... (remaining 2302 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3413 2.80 - 3.33: 12175 3.33 - 3.85: 21216 3.85 - 4.38: 24927 4.38 - 4.90: 46028 Nonbonded interactions: 107759 Sorted by model distance: nonbonded pdb=" OG1 THR B 20 " pdb=" O ALA B 143 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR D 20 " pdb=" O ALA D 143 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR A 20 " pdb=" O ALA A 143 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR E 20 " pdb=" O ALA E 143 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR C 20 " pdb=" O ALA C 143 " model vdw 2.279 3.040 ... (remaining 107754 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 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 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 404 through 405 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 406 or (resid 407 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 C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 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 through 409 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 or (re \ sid 404 through 405 and (name N or name C1 or name C10 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C \ 19 or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C4 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 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 C20 or name C21 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or na \ me 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 407 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 C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 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 through 409 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 or (re \ sid 404 through 405 and (name N or name C1 or name C10 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C \ 19 or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C4 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 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 C20 or name C21 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or na \ me 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 407 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 C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 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 through 409 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 or (re \ sid 404 through 405 and (name N or name C1 or name C10 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C \ 19 or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C4 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 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 C20 or name C21 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or na \ me 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 407 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 C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 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 through 409 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)))) selection = (chain 'E' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 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 404 through 405 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 406 or (resid 407 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 C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 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 through 409 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.510 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14430 Z= 0.136 Angle : 0.522 5.402 19385 Z= 0.277 Chirality : 0.043 0.139 2115 Planarity : 0.005 0.060 2305 Dihedral : 22.283 173.642 5910 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % 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 aren not related in a simple way. whole: 0.24 (0.22), residues: 1555 helix: 2.51 (0.23), residues: 500 sheet: -0.46 (0.27), residues: 445 loop : -1.38 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 133 TYR 0.007 0.001 TYR C 119 PHE 0.023 0.001 PHE B 37 TRP 0.019 0.001 TRP B 72 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00295 (14430) covalent geometry : angle 0.52220 (19385) hydrogen bonds : bond 0.17859 ( 595) hydrogen bonds : angle 6.51949 ( 1840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.444 Fit side-chains REVERT: A 248 LYS cc_start: 0.6697 (tptt) cc_final: 0.6391 (mmtt) REVERT: E 23 TYR cc_start: 0.6433 (t80) cc_final: 0.6211 (t80) REVERT: E 248 LYS cc_start: 0.6755 (tptt) cc_final: 0.6513 (mmtt) REVERT: B 176 LEU cc_start: 0.8014 (tp) cc_final: 0.7802 (mt) REVERT: C 248 LYS cc_start: 0.6654 (tptt) cc_final: 0.6343 (mmmt) REVERT: D 248 LYS cc_start: 0.6795 (tptt) cc_final: 0.6493 (mmtt) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1043 time to fit residues: 49.6335 Evaluate side-chains 171 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 307 ASN E 307 ASN B 307 ASN C 307 ASN D 307 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.181984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.140258 restraints weight = 37901.200| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 3.27 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14430 Z= 0.276 Angle : 0.886 10.323 19385 Z= 0.440 Chirality : 0.055 0.187 2115 Planarity : 0.008 0.078 2305 Dihedral : 23.522 176.554 2965 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.49 % Allowed : 14.31 % Favored : 83.20 % 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 aren not related in a simple way. whole: -0.30 (0.21), residues: 1555 helix: 1.87 (0.21), residues: 505 sheet: -0.22 (0.29), residues: 405 loop : -1.94 (0.21), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 133 TYR 0.023 0.003 TYR A 254 PHE 0.034 0.004 PHE B 37 TRP 0.052 0.008 TRP C 72 HIS 0.004 0.002 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00643 (14430) covalent geometry : angle 0.88640 (19385) hydrogen bonds : bond 0.07621 ( 595) hydrogen bonds : angle 4.81872 ( 1840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.519 Fit side-chains REVERT: B 307 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8623 (m-40) REVERT: C 307 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8548 (m-40) REVERT: D 109 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6936 (ttm110) outliers start: 35 outliers final: 12 residues processed: 195 average time/residue: 0.1162 time to fit residues: 33.7705 Evaluate side-chains 141 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 307 ASN Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 307 ASN Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 307 ASN Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 121 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 67 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 93 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 200 ASN D 307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.181618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.142723 restraints weight = 44616.096| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 4.35 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14430 Z= 0.145 Angle : 0.608 8.404 19385 Z= 0.306 Chirality : 0.046 0.165 2115 Planarity : 0.006 0.052 2305 Dihedral : 22.068 173.564 2965 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.14 % Allowed : 17.22 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.21), residues: 1555 helix: 2.22 (0.21), residues: 535 sheet: -0.03 (0.29), residues: 380 loop : -1.92 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 109 TYR 0.013 0.001 TYR E 102 PHE 0.023 0.001 PHE B 312 TRP 0.018 0.002 TRP A 72 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00326 (14430) covalent geometry : angle 0.60807 (19385) hydrogen bonds : bond 0.05900 ( 595) hydrogen bonds : angle 4.12754 ( 1840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.308 Fit side-chains REVERT: D 101 GLN cc_start: 0.6710 (mp10) cc_final: 0.6286 (mt0) outliers start: 16 outliers final: 10 residues processed: 131 average time/residue: 0.1062 time to fit residues: 21.5327 Evaluate side-chains 122 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 307 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 73 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 ASN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.180494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.139683 restraints weight = 38028.312| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.19 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14430 Z= 0.142 Angle : 0.578 6.227 19385 Z= 0.288 Chirality : 0.046 0.197 2115 Planarity : 0.006 0.056 2305 Dihedral : 20.395 168.167 2965 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.57 % Allowed : 16.65 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.22), residues: 1555 helix: 2.49 (0.21), residues: 535 sheet: -0.18 (0.28), residues: 425 loop : -1.73 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 109 TYR 0.013 0.001 TYR C 102 PHE 0.019 0.001 PHE B 37 TRP 0.020 0.002 TRP A 47 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00322 (14430) covalent geometry : angle 0.57758 (19385) hydrogen bonds : bond 0.05468 ( 595) hydrogen bonds : angle 3.90839 ( 1840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.512 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 122 average time/residue: 0.1215 time to fit residues: 22.4141 Evaluate side-chains 104 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 295 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.173567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129638 restraints weight = 31446.147| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.71 r_work: 0.3301 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.7378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.166 14430 Z= 0.246 Angle : 0.667 9.615 19385 Z= 0.337 Chirality : 0.049 0.188 2115 Planarity : 0.006 0.053 2305 Dihedral : 20.537 169.134 2965 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.06 % Allowed : 16.30 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.22), residues: 1555 helix: 2.25 (0.21), residues: 535 sheet: -0.22 (0.27), residues: 430 loop : -1.83 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 62 TYR 0.023 0.002 TYR A 186 PHE 0.021 0.002 PHE A 312 TRP 0.016 0.002 TRP D 72 HIS 0.007 0.002 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00604 (14430) covalent geometry : angle 0.66739 (19385) hydrogen bonds : bond 0.07902 ( 595) hydrogen bonds : angle 4.37080 ( 1840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.456 Fit side-chains REVERT: A 241 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8046 (tt) REVERT: E 305 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8607 (mp) REVERT: C 92 ILE cc_start: 0.6665 (OUTLIER) cc_final: 0.5837 (mp) REVERT: D 109 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7791 (ttm110) REVERT: D 241 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8049 (tt) outliers start: 29 outliers final: 15 residues processed: 107 average time/residue: 0.1136 time to fit residues: 18.8266 Evaluate side-chains 96 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 chunk 128 optimal weight: 9.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 ASN D 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.170866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123079 restraints weight = 41703.654| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.55 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.7523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14430 Z= 0.108 Angle : 0.536 6.124 19385 Z= 0.266 Chirality : 0.044 0.186 2115 Planarity : 0.005 0.047 2305 Dihedral : 19.530 168.151 2965 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.93 % Allowed : 18.15 % Favored : 80.93 % 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 aren not related in a simple way. whole: 0.57 (0.22), residues: 1555 helix: 2.92 (0.21), residues: 530 sheet: -0.08 (0.27), residues: 430 loop : -1.71 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 109 TYR 0.009 0.001 TYR D 66 PHE 0.018 0.001 PHE B 37 TRP 0.022 0.002 TRP D 72 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00239 (14430) covalent geometry : angle 0.53572 (19385) hydrogen bonds : bond 0.04788 ( 595) hydrogen bonds : angle 3.74678 ( 1840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.402 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 87 average time/residue: 0.1209 time to fit residues: 16.2272 Evaluate side-chains 81 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 307 ASN Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 307 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 32 optimal weight: 6.9990 chunk 68 optimal weight: 0.0770 chunk 124 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.168219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120467 restraints weight = 39694.754| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.56 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.7694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14430 Z= 0.140 Angle : 0.559 6.065 19385 Z= 0.280 Chirality : 0.045 0.188 2115 Planarity : 0.005 0.047 2305 Dihedral : 19.290 168.325 2965 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.28 % Allowed : 17.72 % Favored : 81.00 % 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 aren not related in a simple way. whole: 0.60 (0.22), residues: 1555 helix: 2.89 (0.21), residues: 525 sheet: 0.02 (0.28), residues: 425 loop : -1.66 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 109 TYR 0.012 0.001 TYR C 102 PHE 0.022 0.001 PHE D 312 TRP 0.015 0.001 TRP D 72 HIS 0.003 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00333 (14430) covalent geometry : angle 0.55919 (19385) hydrogen bonds : bond 0.05601 ( 595) hydrogen bonds : angle 3.81021 ( 1840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.508 Fit side-chains REVERT: A 92 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6068 (mp) REVERT: C 92 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6098 (mp) outliers start: 18 outliers final: 12 residues processed: 80 average time/residue: 0.1234 time to fit residues: 15.0543 Evaluate side-chains 82 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 307 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 72 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 140 optimal weight: 0.0040 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 135 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 ASN ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.170825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.123625 restraints weight = 43811.311| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.75 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.7771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14430 Z= 0.107 Angle : 0.531 5.972 19385 Z= 0.266 Chirality : 0.044 0.188 2115 Planarity : 0.005 0.044 2305 Dihedral : 18.705 168.158 2965 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.00 % Allowed : 18.22 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.22), residues: 1555 helix: 3.00 (0.21), residues: 530 sheet: 0.07 (0.28), residues: 425 loop : -1.58 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 109 TYR 0.009 0.001 TYR C 102 PHE 0.018 0.001 PHE B 37 TRP 0.016 0.001 TRP D 72 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00238 (14430) covalent geometry : angle 0.53111 (19385) hydrogen bonds : bond 0.04552 ( 595) hydrogen bonds : angle 3.64164 ( 1840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.523 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 79 average time/residue: 0.1237 time to fit residues: 14.9960 Evaluate side-chains 78 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 307 ASN Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 307 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 144 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 307 ASN ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.164442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.114692 restraints weight = 29990.650| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.13 r_work: 0.3114 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.8045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14430 Z= 0.202 Angle : 0.617 5.840 19385 Z= 0.309 Chirality : 0.048 0.195 2115 Planarity : 0.006 0.048 2305 Dihedral : 19.042 169.851 2965 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.28 % Allowed : 17.51 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.22), residues: 1555 helix: 2.51 (0.21), residues: 535 sheet: 0.07 (0.28), residues: 425 loop : -1.65 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 109 TYR 0.015 0.001 TYR E 102 PHE 0.028 0.002 PHE D 312 TRP 0.011 0.002 TRP D 72 HIS 0.005 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00496 (14430) covalent geometry : angle 0.61652 (19385) hydrogen bonds : bond 0.06746 ( 595) hydrogen bonds : angle 3.97119 ( 1840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.394 Fit side-chains REVERT: A 92 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.6057 (mp) REVERT: B 92 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6236 (mp) REVERT: C 92 ILE cc_start: 0.6700 (OUTLIER) cc_final: 0.5907 (mp) outliers start: 18 outliers final: 11 residues processed: 85 average time/residue: 0.1480 time to fit residues: 18.0087 Evaluate side-chains 78 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 252 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 114 optimal weight: 0.0470 chunk 143 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.166028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.120107 restraints weight = 35557.287| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.23 r_work: 0.3065 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.8165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14430 Z= 0.149 Angle : 0.575 6.295 19385 Z= 0.289 Chirality : 0.046 0.192 2115 Planarity : 0.005 0.049 2305 Dihedral : 18.859 169.606 2965 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.07 % Allowed : 18.15 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.22), residues: 1555 helix: 2.78 (0.21), residues: 535 sheet: 0.08 (0.28), residues: 425 loop : -1.61 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 109 TYR 0.012 0.001 TYR C 102 PHE 0.019 0.001 PHE C 312 TRP 0.016 0.002 TRP D 72 HIS 0.003 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00359 (14430) covalent geometry : angle 0.57541 (19385) hydrogen bonds : bond 0.05837 ( 595) hydrogen bonds : angle 3.83156 ( 1840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.510 Fit side-chains REVERT: A 92 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6134 (mp) REVERT: B 92 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6195 (mp) REVERT: C 92 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.5880 (mp) outliers start: 15 outliers final: 12 residues processed: 75 average time/residue: 0.1276 time to fit residues: 14.6021 Evaluate side-chains 78 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 307 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 117 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.166298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.120072 restraints weight = 48053.330| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 4.14 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.8171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 14430 Z= 0.152 Angle : 0.786 59.183 19385 Z= 0.438 Chirality : 0.045 0.188 2115 Planarity : 0.005 0.049 2305 Dihedral : 18.851 169.578 2965 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.00 % Allowed : 18.22 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.22), residues: 1555 helix: 2.77 (0.21), residues: 535 sheet: 0.08 (0.28), residues: 425 loop : -1.61 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 109 TYR 0.012 0.001 TYR C 102 PHE 0.019 0.001 PHE C 312 TRP 0.016 0.001 TRP D 72 HIS 0.003 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00318 (14430) covalent geometry : angle 0.78626 (19385) hydrogen bonds : bond 0.05762 ( 595) hydrogen bonds : angle 3.84551 ( 1840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2764.57 seconds wall clock time: 48 minutes 17.03 seconds (2897.03 seconds total)