Starting phenix.real_space_refine on Wed Feb 4 22:47:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9laj_62930/02_2026/9laj_62930.cif Found real_map, /net/cci-nas-00/data/ceres_data/9laj_62930/02_2026/9laj_62930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9laj_62930/02_2026/9laj_62930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9laj_62930/02_2026/9laj_62930.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9laj_62930/02_2026/9laj_62930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9laj_62930/02_2026/9laj_62930.map" } resolution = 3.16 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 19 5.49 5 S 20 5.16 5 Cl 5 4.86 5 C 8849 2.51 5 N 2039 2.21 5 O 2424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13356 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "D" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 Chain: "E" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "C" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 162 Unusual residues: {' CL': 1, 'PEE': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' CL': 1, 'PEE': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 71 Chain: "D" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 176 Unusual residues: {' CL': 1, 'PEE': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 148 Unusual residues: {' CL': 1, 'PEE': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {' CL': 1, 'PEE': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 44 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG D 293 " occ=0.52 ... (20 atoms not shown) pdb=" NH2BARG D 293 " occ=0.48 residue: pdb=" N AARG C 293 " occ=0.52 ... (20 atoms not shown) pdb=" NH2BARG C 293 " occ=0.48 Time building chain proxies: 4.44, per 1000 atoms: 0.33 Number of scatterers: 13356 At special positions: 0 Unit cell: (101.08, 94.24, 129.96, 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 19 15.00 O 2424 8.00 N 2039 7.00 C 8849 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: 1.21 Conformation dependent library (CDL) restraints added in 948.3 milliseconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3054 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 18 sheets defined 38.2% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 196 through 213 removed outlier: 5.014A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.537A pdb=" N TRP A 217 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 218' Processing helix chain 'A' and resid 220 through 245 removed outlier: 3.824A pdb=" N THR A 244 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASN A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.816A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.954A pdb=" N ILE B 71 " --> pdb=" O PRO B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 196 through 214 removed outlier: 4.973A pdb=" N LEU B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 215 through 218 removed outlier: 3.689A pdb=" N SER B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 215 through 218' Processing helix chain 'B' and resid 220 through 244 removed outlier: 4.106A pdb=" N THR B 244 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 284 through 315 removed outlier: 3.807A pdb=" N ARG B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 194 through 198 Processing helix chain 'D' and resid 201 through 213 Processing helix chain 'D' and resid 214 through 218 removed outlier: 3.578A pdb=" N SER D 218 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 245 removed outlier: 3.579A pdb=" N ALA D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN D 245 " --> pdb=" O LEU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 282 removed outlier: 3.794A pdb=" N ALA D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 316 removed outlier: 3.649A pdb=" N ALA D 288 " --> pdb=" O GLN D 284 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE D 297 " --> pdb=" O AARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing helix chain 'E' and resid 50 through 53 removed outlier: 3.696A pdb=" N ALA E 53 " --> pdb=" O ARG E 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 50 through 53' Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 196 through 214 removed outlier: 3.646A pdb=" N ASN E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU E 203 " --> pdb=" O PRO E 199 " (cutoff:3.500A) Proline residue: E 204 - end of helix Processing helix chain 'E' and resid 215 through 218 removed outlier: 3.627A pdb=" N SER E 218 " --> pdb=" O ALA E 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 215 through 218' Processing helix chain 'E' and resid 220 through 244 Processing helix chain 'E' and resid 253 through 282 removed outlier: 3.856A pdb=" N ALA E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 316 removed outlier: 3.647A pdb=" N ALA E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.721A pdb=" N ILE C 71 " --> pdb=" O PRO C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 146 through 149 Processing helix chain 'C' and resid 196 through 213 removed outlier: 5.287A pdb=" N LEU C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Proline residue: C 204 - end of helix Processing helix chain 'C' and resid 214 through 218 removed outlier: 3.683A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 244 removed outlier: 3.596A pdb=" N ILE C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 284 through 315 removed outlier: 3.716A pdb=" N ALA C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 297 " --> pdb=" O AARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 5.727A pdb=" N ALA A 87 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N SER A 107 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 100 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TRP A 47 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 45 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 141 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 removed outlier: 5.727A pdb=" N ALA A 87 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N SER A 107 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 100 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TRP A 47 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 45 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR A 36 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU A 30 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 28 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU A 24 " --> pdb=" O PHE A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.962A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 24 through 28 removed outlier: 5.886A pdb=" N LEU B 24 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE B 42 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 43 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU B 45 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR B 102 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN B 101 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE B 92 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU B 103 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 28 removed outlier: 5.886A pdb=" N LEU B 24 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE B 42 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA B 143 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.618A pdb=" N LEU B 184 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL B 132 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER B 182 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER B 164 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER B 191 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE B 162 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 16 through 20 removed outlier: 6.374A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ALA D 143 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL D 18 " --> pdb=" O ALA D 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 88 through 94 removed outlier: 5.737A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 93 " --> pdb=" O GLN D 101 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP D 47 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR D 36 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER D 29 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N CYS D 27 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASN D 40 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR D 23 " --> pdb=" O PHE D 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 76 through 78 removed outlier: 3.598A pdb=" N SER D 182 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 76 through 78 removed outlier: 3.598A pdb=" N SER D 182 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 86 through 94 removed outlier: 5.905A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS E 48 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR E 17 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 86 through 94 removed outlier: 5.905A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS E 48 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR E 17 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 77 through 78 removed outlier: 3.504A pdb=" N ILE E 190 " --> pdb=" O GLN E 124 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER E 182 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 77 through 78 removed outlier: 3.504A pdb=" N ILE E 190 " --> pdb=" O GLN E 124 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER E 182 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 64 through 65 removed outlier: 7.288A pdb=" N LYS C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N CYS C 27 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ASN C 40 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR C 23 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 21 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LYS C 48 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C 17 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 64 through 65 removed outlier: 7.288A pdb=" N LYS C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N CYS C 27 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ASN C 40 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR C 23 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 21 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LYS C 48 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C 17 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 76 through 78 removed outlier: 4.256A pdb=" N ASP C 185 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER C 164 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER C 191 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE C 162 " --> pdb=" O SER C 191 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 174 through 176 680 hydrogen bonds defined for protein. 1949 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: 2.22 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2163 1.33 - 1.45: 3641 1.45 - 1.57: 7793 1.57 - 1.69: 38 1.69 - 1.81: 35 Bond restraints: 13670 Sorted by residual: bond pdb=" CB TRP E 213 " pdb=" CG TRP E 213 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.48e+00 bond pdb=" C13 PEE A 404 " pdb=" C14 PEE A 404 " ideal model delta sigma weight residual 1.524 1.504 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" C26 PEE D 403 " pdb=" C27 PEE D 403 " ideal model delta sigma weight residual 1.522 1.503 0.019 2.00e-02 2.50e+03 8.63e-01 bond pdb=" CB THR B 231 " pdb=" CG2 THR B 231 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.95e-01 bond pdb=" CB THR A 231 " pdb=" CG2 THR A 231 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.70e-01 ... (remaining 13665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 18314 1.72 - 3.44: 186 3.44 - 5.16: 31 5.16 - 6.88: 4 6.88 - 8.59: 1 Bond angle restraints: 18536 Sorted by residual: angle pdb=" C ARG A 50 " pdb=" N ARG A 51 " pdb=" CA ARG A 51 " ideal model delta sigma weight residual 121.54 126.74 -5.20 1.91e+00 2.74e-01 7.42e+00 angle pdb=" N ASN C 245 " pdb=" CA ASN C 245 " pdb=" C ASN C 245 " ideal model delta sigma weight residual 114.56 111.94 2.62 1.27e+00 6.20e-01 4.24e+00 angle pdb=" N VAL C 169 " pdb=" CA VAL C 169 " pdb=" C VAL C 169 " ideal model delta sigma weight residual 112.98 110.42 2.56 1.25e+00 6.40e-01 4.19e+00 angle pdb=" CA ASN C 245 " pdb=" C ASN C 245 " pdb=" N LEU C 246 " ideal model delta sigma weight residual 119.26 117.09 2.17 1.14e+00 7.69e-01 3.64e+00 angle pdb=" N LEU E 203 " pdb=" CA LEU E 203 " pdb=" C LEU E 203 " ideal model delta sigma weight residual 109.81 113.93 -4.12 2.21e+00 2.05e-01 3.47e+00 ... (remaining 18531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.32: 8027 32.32 - 64.64: 177 64.64 - 96.96: 33 96.96 - 129.29: 13 129.29 - 161.61: 14 Dihedral angle restraints: 8264 sinusoidal: 3576 harmonic: 4688 Sorted by residual: dihedral pdb=" C3 PEE E 402 " pdb=" C1 PEE E 402 " pdb=" C2 PEE E 402 " pdb=" O3P PEE E 402 " ideal model delta sinusoidal sigma weight residual 62.73 -135.66 -161.61 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" N PEE C 404 " pdb=" C4 PEE C 404 " pdb=" C5 PEE C 404 " pdb=" O4P PEE C 404 " ideal model delta sinusoidal sigma weight residual -56.97 102.16 -159.13 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" O2 PEE E 402 " pdb=" C1 PEE E 402 " pdb=" C2 PEE E 402 " pdb=" O3P PEE E 402 " ideal model delta sinusoidal sigma weight residual -59.96 98.93 -158.89 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 8261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1245 0.027 - 0.054: 473 0.054 - 0.081: 190 0.081 - 0.108: 145 0.108 - 0.135: 43 Chirality restraints: 2096 Sorted by residual: chirality pdb=" CA ILE E 128 " pdb=" N ILE E 128 " pdb=" C ILE E 128 " pdb=" CB ILE E 128 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE C 128 " pdb=" N ILE C 128 " pdb=" C ILE C 128 " pdb=" CB ILE C 128 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE B 128 " pdb=" N ILE B 128 " pdb=" C ILE B 128 " pdb=" CB ILE B 128 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 2093 not shown) Planarity restraints: 2269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 249 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO C 250 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 250 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 250 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 55 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.99e+00 pdb=" N PRO D 56 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 56 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 56 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 249 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 250 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 250 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 250 " -0.019 5.00e-02 4.00e+02 ... (remaining 2266 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 493 2.72 - 3.27: 12706 3.27 - 3.81: 20180 3.81 - 4.36: 24702 4.36 - 4.90: 44383 Nonbonded interactions: 102464 Sorted by model distance: nonbonded pdb=" O LEU A 227 " pdb=" OG1 THR A 231 " model vdw 2.178 3.040 nonbonded pdb=" NH1 ARG D 133 " pdb=" OE2 GLU D 181 " model vdw 2.238 3.120 nonbonded pdb=" O LEU D 241 " pdb=" OG1 THR D 244 " model vdw 2.240 3.040 nonbonded pdb=" O LEU B 227 " pdb=" OG1 THR B 231 " model vdw 2.248 3.040 nonbonded pdb=" OE2 GLU C 163 " pdb=" OG SER C 191 " model vdw 2.260 3.040 ... (remaining 102459 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 292 or resid 294 through 316)) selection = (chain 'B' and (resid 5 through 292 or resid 294 through 316)) selection = (chain 'C' and (resid 5 through 292 or resid 294 through 316)) selection = (chain 'D' and (resid 5 through 292 or resid 294 through 316)) selection = (chain 'E' and (resid 5 through 292 or resid 294 through 316)) } 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: 2.760 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.100 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 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 : 0.002 0.038 13670 Z= 0.108 Angle : 0.488 8.594 18536 Z= 0.250 Chirality : 0.042 0.135 2096 Planarity : 0.004 0.037 2269 Dihedral : 16.673 161.607 5210 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.64 % Allowed : 4.49 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.22), residues: 1556 helix: 3.42 (0.21), residues: 512 sheet: -0.43 (0.26), residues: 414 loop : -1.27 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 109 TYR 0.015 0.001 TYR A 254 PHE 0.009 0.001 PHE A 174 TRP 0.005 0.001 TRP A 160 HIS 0.003 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00223 (13670) covalent geometry : angle 0.48751 (18536) hydrogen bonds : bond 0.18528 ( 597) hydrogen bonds : angle 7.15987 ( 1949) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 0.511 Fit side-chains REVERT: A 248 LYS cc_start: 0.8972 (mptt) cc_final: 0.8271 (mptt) REVERT: B 147 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7132 (tm-30) REVERT: D 205 MET cc_start: 0.8491 (mmt) cc_final: 0.8175 (mmt) REVERT: E 174 PHE cc_start: 0.8245 (p90) cc_final: 0.7945 (p90) REVERT: C 35 GLU cc_start: 0.8935 (pt0) cc_final: 0.8701 (pt0) outliers start: 9 outliers final: 6 residues processed: 176 average time/residue: 0.1246 time to fit residues: 32.1392 Evaluate side-chains 149 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 52 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.0570 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.0470 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN C 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.165000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.112927 restraints weight = 35081.654| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 4.63 r_work: 0.2871 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13670 Z= 0.111 Angle : 0.538 9.499 18536 Z= 0.276 Chirality : 0.044 0.169 2096 Planarity : 0.004 0.067 2269 Dihedral : 18.850 158.713 2289 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.00 % Allowed : 7.63 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.22), residues: 1556 helix: 3.46 (0.21), residues: 515 sheet: -0.12 (0.26), residues: 410 loop : -1.26 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 TYR 0.012 0.001 TYR A 254 PHE 0.014 0.001 PHE B 37 TRP 0.005 0.001 TRP C 47 HIS 0.003 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00223 (13670) covalent geometry : angle 0.53824 (18536) hydrogen bonds : bond 0.04884 ( 597) hydrogen bonds : angle 4.78893 ( 1949) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.500 Fit side-chains REVERT: A 248 LYS cc_start: 0.8938 (mptt) cc_final: 0.8261 (mptt) REVERT: B 147 GLU cc_start: 0.7319 (tm-30) cc_final: 0.7075 (tm-30) REVERT: B 161 ASP cc_start: 0.7849 (p0) cc_final: 0.7569 (p0) REVERT: D 205 MET cc_start: 0.8708 (mmt) cc_final: 0.8150 (mmt) REVERT: E 88 ASP cc_start: 0.8577 (p0) cc_final: 0.8121 (p0) outliers start: 14 outliers final: 13 residues processed: 176 average time/residue: 0.1155 time to fit residues: 29.8316 Evaluate side-chains 157 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 26 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN D 200 ASN ** D 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 = 0.3718 r_free = 0.3718 target = 0.155706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.099500 restraints weight = 38919.986| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.71 r_work: 0.2741 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13670 Z= 0.198 Angle : 0.592 8.908 18536 Z= 0.302 Chirality : 0.045 0.152 2096 Planarity : 0.004 0.061 2269 Dihedral : 18.512 159.836 2286 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.93 % Allowed : 8.63 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.21), residues: 1556 helix: 3.25 (0.21), residues: 503 sheet: -0.04 (0.25), residues: 416 loop : -1.34 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 105 TYR 0.015 0.002 TYR A 254 PHE 0.014 0.002 PHE B 195 TRP 0.012 0.002 TRP B 213 HIS 0.005 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00487 (13670) covalent geometry : angle 0.59232 (18536) hydrogen bonds : bond 0.07620 ( 597) hydrogen bonds : angle 4.75107 ( 1949) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.552 Fit side-chains REVERT: B 133 ARG cc_start: 0.6020 (mtp180) cc_final: 0.5739 (mtp-110) REVERT: B 147 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7190 (tm-30) REVERT: D 180 LEU cc_start: 0.8192 (tt) cc_final: 0.7986 (tt) REVERT: D 205 MET cc_start: 0.8715 (mmt) cc_final: 0.8150 (mmt) REVERT: E 88 ASP cc_start: 0.8705 (p0) cc_final: 0.8209 (p0) REVERT: C 102 TYR cc_start: 0.8810 (t80) cc_final: 0.8569 (t80) outliers start: 27 outliers final: 20 residues processed: 168 average time/residue: 0.1268 time to fit residues: 31.1734 Evaluate side-chains 167 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 166 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 39 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 ASN ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.158206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.103437 restraints weight = 36151.339| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 4.06 r_work: 0.2752 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13670 Z= 0.177 Angle : 0.568 8.533 18536 Z= 0.290 Chirality : 0.044 0.147 2096 Planarity : 0.004 0.059 2269 Dihedral : 18.015 161.051 2283 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.14 % Allowed : 9.20 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.21), residues: 1556 helix: 3.26 (0.21), residues: 503 sheet: 0.06 (0.25), residues: 416 loop : -1.38 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 118 TYR 0.013 0.001 TYR A 102 PHE 0.015 0.001 PHE B 312 TRP 0.009 0.001 TRP A 47 HIS 0.003 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00432 (13670) covalent geometry : angle 0.56840 (18536) hydrogen bonds : bond 0.07013 ( 597) hydrogen bonds : angle 4.54846 ( 1949) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.543 Fit side-chains REVERT: B 133 ARG cc_start: 0.6052 (mtp180) cc_final: 0.5793 (mtp-110) REVERT: B 147 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7152 (tm-30) REVERT: B 161 ASP cc_start: 0.7671 (p0) cc_final: 0.7448 (p0) REVERT: D 205 MET cc_start: 0.8643 (mmt) cc_final: 0.8125 (mmt) REVERT: E 75 GLU cc_start: 0.7487 (pp20) cc_final: 0.7002 (pp20) REVERT: E 88 ASP cc_start: 0.8812 (p0) cc_final: 0.8301 (p0) outliers start: 30 outliers final: 23 residues processed: 168 average time/residue: 0.1308 time to fit residues: 31.8896 Evaluate side-chains 171 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 166 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 38 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 = 0.3776 r_free = 0.3776 target = 0.159753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107743 restraints weight = 30443.744| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.70 r_work: 0.2772 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13670 Z= 0.139 Angle : 0.544 8.435 18536 Z= 0.277 Chirality : 0.044 0.143 2096 Planarity : 0.004 0.071 2269 Dihedral : 17.641 161.171 2283 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.07 % Allowed : 9.77 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.22), residues: 1556 helix: 3.38 (0.21), residues: 503 sheet: 0.18 (0.25), residues: 416 loop : -1.37 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 109 TYR 0.017 0.001 TYR C 251 PHE 0.015 0.001 PHE B 312 TRP 0.009 0.001 TRP A 47 HIS 0.003 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00321 (13670) covalent geometry : angle 0.54365 (18536) hydrogen bonds : bond 0.06367 ( 597) hydrogen bonds : angle 4.40181 ( 1949) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.532 Fit side-chains REVERT: B 133 ARG cc_start: 0.5977 (mtp180) cc_final: 0.5741 (mtp-110) REVERT: B 147 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7028 (tm-30) REVERT: B 161 ASP cc_start: 0.7560 (p0) cc_final: 0.7352 (p0) REVERT: D 205 MET cc_start: 0.8576 (mmt) cc_final: 0.8041 (mmt) REVERT: E 75 GLU cc_start: 0.7472 (pp20) cc_final: 0.6981 (pp20) REVERT: E 88 ASP cc_start: 0.8815 (p0) cc_final: 0.8289 (p0) REVERT: C 102 TYR cc_start: 0.8596 (t80) cc_final: 0.8345 (t80) outliers start: 29 outliers final: 23 residues processed: 173 average time/residue: 0.1261 time to fit residues: 31.9569 Evaluate side-chains 169 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 166 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 120 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 = 0.3776 r_free = 0.3776 target = 0.159341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.105314 restraints weight = 35002.565| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 4.27 r_work: 0.2771 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13670 Z= 0.175 Angle : 0.564 8.014 18536 Z= 0.288 Chirality : 0.044 0.153 2096 Planarity : 0.004 0.065 2269 Dihedral : 17.516 162.886 2283 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.92 % Allowed : 9.56 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1556 helix: 3.25 (0.21), residues: 503 sheet: 0.16 (0.25), residues: 416 loop : -1.40 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 109 TYR 0.017 0.001 TYR C 251 PHE 0.012 0.001 PHE A 37 TRP 0.010 0.001 TRP A 47 HIS 0.003 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00429 (13670) covalent geometry : angle 0.56388 (18536) hydrogen bonds : bond 0.07011 ( 597) hydrogen bonds : angle 4.45776 ( 1949) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: B 147 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7098 (tm-30) REVERT: D 205 MET cc_start: 0.8729 (mmt) cc_final: 0.8263 (mmt) REVERT: E 75 GLU cc_start: 0.7509 (pp20) cc_final: 0.7021 (pp20) REVERT: E 88 ASP cc_start: 0.8922 (p0) cc_final: 0.8382 (p0) REVERT: C 102 TYR cc_start: 0.8680 (t80) cc_final: 0.8441 (t80) outliers start: 41 outliers final: 29 residues processed: 172 average time/residue: 0.1228 time to fit residues: 30.8003 Evaluate side-chains 172 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 166 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 109 optimal weight: 0.8980 chunk 5 optimal weight: 0.0270 chunk 110 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 77 optimal weight: 0.0670 chunk 96 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 = 0.3810 r_free = 0.3810 target = 0.162388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.110036 restraints weight = 44118.964| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 4.17 r_work: 0.2807 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13670 Z= 0.120 Angle : 0.529 8.404 18536 Z= 0.269 Chirality : 0.043 0.140 2096 Planarity : 0.004 0.061 2269 Dihedral : 16.927 162.757 2280 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.00 % Allowed : 10.34 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.22), residues: 1556 helix: 3.49 (0.21), residues: 503 sheet: 0.27 (0.26), residues: 416 loop : -1.35 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 109 TYR 0.014 0.001 TYR C 251 PHE 0.014 0.001 PHE B 312 TRP 0.008 0.001 TRP C 47 HIS 0.003 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00268 (13670) covalent geometry : angle 0.52857 (18536) hydrogen bonds : bond 0.05586 ( 597) hydrogen bonds : angle 4.20123 ( 1949) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.565 Fit side-chains REVERT: A 145 ASP cc_start: 0.7044 (p0) cc_final: 0.6819 (p0) REVERT: B 147 GLU cc_start: 0.7358 (tm-30) cc_final: 0.7028 (tm-30) REVERT: D 205 MET cc_start: 0.8615 (mmt) cc_final: 0.8121 (mmt) REVERT: E 75 GLU cc_start: 0.7469 (pp20) cc_final: 0.6978 (pp20) REVERT: E 88 ASP cc_start: 0.8856 (p0) cc_final: 0.8633 (p0) outliers start: 28 outliers final: 24 residues processed: 168 average time/residue: 0.1146 time to fit residues: 28.3613 Evaluate side-chains 165 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 19 optimal weight: 4.9990 chunk 144 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3756 r_free = 0.3756 target = 0.157942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.103104 restraints weight = 41390.776| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.70 r_work: 0.2772 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13670 Z= 0.175 Angle : 0.565 8.039 18536 Z= 0.289 Chirality : 0.044 0.158 2096 Planarity : 0.004 0.074 2269 Dihedral : 16.994 164.408 2280 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.14 % Allowed : 10.41 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.21), residues: 1556 helix: 3.29 (0.21), residues: 503 sheet: 0.21 (0.25), residues: 416 loop : -1.40 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 109 TYR 0.016 0.001 TYR C 251 PHE 0.017 0.001 PHE B 312 TRP 0.010 0.001 TRP A 47 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00429 (13670) covalent geometry : angle 0.56513 (18536) hydrogen bonds : bond 0.06921 ( 597) hydrogen bonds : angle 4.37625 ( 1949) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.609 Fit side-chains REVERT: B 147 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7076 (tm-30) REVERT: D 205 MET cc_start: 0.8669 (mmt) cc_final: 0.8185 (mmt) REVERT: E 75 GLU cc_start: 0.7467 (pp20) cc_final: 0.6959 (pp20) outliers start: 30 outliers final: 28 residues processed: 162 average time/residue: 0.1202 time to fit residues: 28.6933 Evaluate side-chains 167 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 166 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 52 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 67 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 = 0.3793 r_free = 0.3793 target = 0.161075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.106729 restraints weight = 34868.838| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.82 r_work: 0.2798 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13670 Z= 0.132 Angle : 0.534 8.163 18536 Z= 0.272 Chirality : 0.043 0.145 2096 Planarity : 0.004 0.075 2269 Dihedral : 16.553 164.451 2280 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.14 % Allowed : 10.56 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.21), residues: 1556 helix: 3.43 (0.21), residues: 503 sheet: 0.29 (0.25), residues: 416 loop : -1.36 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 109 TYR 0.014 0.001 TYR C 251 PHE 0.016 0.001 PHE B 312 TRP 0.008 0.001 TRP A 47 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00307 (13670) covalent geometry : angle 0.53416 (18536) hydrogen bonds : bond 0.05860 ( 597) hydrogen bonds : angle 4.19189 ( 1949) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.347 Fit side-chains REVERT: B 147 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7018 (tm-30) REVERT: D 205 MET cc_start: 0.8582 (mmt) cc_final: 0.8127 (mmt) REVERT: E 75 GLU cc_start: 0.7451 (pp20) cc_final: 0.6948 (pp20) outliers start: 30 outliers final: 29 residues processed: 160 average time/residue: 0.1076 time to fit residues: 25.5814 Evaluate side-chains 168 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 166 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 = 0.3784 r_free = 0.3784 target = 0.159918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.107989 restraints weight = 45836.427| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 4.34 r_work: 0.2772 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13670 Z= 0.163 Angle : 0.555 7.937 18536 Z= 0.283 Chirality : 0.044 0.154 2096 Planarity : 0.004 0.073 2269 Dihedral : 16.590 165.830 2280 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.21 % Allowed : 10.56 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.21), residues: 1556 helix: 3.31 (0.21), residues: 503 sheet: 0.22 (0.25), residues: 412 loop : -1.36 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 118 TYR 0.015 0.001 TYR C 251 PHE 0.018 0.001 PHE B 312 TRP 0.009 0.001 TRP A 47 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00393 (13670) covalent geometry : angle 0.55469 (18536) hydrogen bonds : bond 0.06619 ( 597) hydrogen bonds : angle 4.29061 ( 1949) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.321 Fit side-chains REVERT: B 147 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7076 (tm-30) REVERT: D 205 MET cc_start: 0.8708 (mmt) cc_final: 0.8268 (mmt) REVERT: E 75 GLU cc_start: 0.7511 (pp20) cc_final: 0.7013 (pp20) outliers start: 31 outliers final: 31 residues processed: 157 average time/residue: 0.1276 time to fit residues: 29.2058 Evaluate side-chains 167 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 166 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 = 0.3746 r_free = 0.3746 target = 0.156699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104379 restraints weight = 30927.564| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.57 r_work: 0.2725 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13670 Z= 0.240 Angle : 0.622 8.293 18536 Z= 0.318 Chirality : 0.046 0.174 2096 Planarity : 0.005 0.073 2269 Dihedral : 17.033 167.813 2280 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.28 % Allowed : 10.56 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.21), residues: 1556 helix: 3.06 (0.21), residues: 503 sheet: 0.12 (0.25), residues: 416 loop : -1.48 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 109 TYR 0.016 0.002 TYR C 251 PHE 0.019 0.002 PHE B 312 TRP 0.012 0.002 TRP B 213 HIS 0.005 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00600 (13670) covalent geometry : angle 0.62157 (18536) hydrogen bonds : bond 0.08045 ( 597) hydrogen bonds : angle 4.54849 ( 1949) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3583.76 seconds wall clock time: 61 minutes 57.44 seconds (3717.44 seconds total)