Starting phenix.real_space_refine on Wed Mar 4 11:02:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lbc_62940/03_2026/9lbc_62940.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lbc_62940/03_2026/9lbc_62940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lbc_62940/03_2026/9lbc_62940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lbc_62940/03_2026/9lbc_62940.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lbc_62940/03_2026/9lbc_62940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lbc_62940/03_2026/9lbc_62940.map" } resolution = 3.4 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 20 5.16 5 C 8463 2.51 5 N 2038 2.21 5 O 2305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12830 Number of models: 1 Model: "" Number of chains: 8 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: "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: "A" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 Chain: "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: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 50 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: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 43 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 14 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG C 293 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG C 293 " occ=0.47 residue: pdb=" N AARG D 293 " occ=0.45 ... (20 atoms not shown) pdb=" NH2BARG D 293 " occ=0.55 residue: pdb=" N AARG A 293 " occ=0.61 ... (20 atoms not shown) pdb=" NH2BARG A 293 " occ=0.39 Time building chain proxies: 4.53, per 1000 atoms: 0.35 Number of scatterers: 12830 At special positions: 0 Unit cell: (92.72, 95, 130.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 4 15.00 O 2305 8.00 N 2038 7.00 C 8463 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: 1.03 Conformation dependent library (CDL) restraints added in 1.0 seconds 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 17 sheets defined 37.9% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 196 through 213 removed outlier: 5.264A 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: 3.705A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 246 removed outlier: 3.778A pdb=" N ILE C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 284 through 315 removed outlier: 3.640A pdb=" N ALA C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE C 297 " --> pdb=" O AARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 196 through 201 removed outlier: 3.702A pdb=" N ASN D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 213 Processing helix chain 'D' and resid 214 through 218 Processing helix chain 'D' and resid 220 through 244 Processing helix chain 'D' and resid 254 through 282 Processing helix chain 'D' and resid 284 through 316 removed outlier: 3.823A 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: 3.905A 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 201 Processing helix chain 'E' and resid 201 through 214 removed outlier: 3.608A pdb=" N MET E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 218 removed outlier: 3.538A 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: 3.746A pdb=" N ALA E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 316 removed outlier: 3.634A pdb=" N ALA E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 201 through 213 removed outlier: 4.095A pdb=" N MET A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.880A pdb=" N SER A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 243 Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 314 removed outlier: 3.540A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 297 " --> pdb=" O AARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 50 through 53 removed outlier: 3.812A pdb=" N ALA B 53 " --> pdb=" O ARG B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 53' Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 196 through 214 removed outlier: 3.639A pdb=" N ASN B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 4.963A 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: 3.743A 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 Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 284 through 315 removed outlier: 3.621A pdb=" N ALA B 288 " --> pdb=" O GLN B 284 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.706A pdb=" N LYS C 64 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP C 47 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR C 36 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER C 29 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N CYS C 27 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN C 40 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 21 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS C 48 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR C 17 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.706A pdb=" N LYS C 64 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP C 47 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR C 36 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER C 29 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N CYS C 27 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN C 40 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 21 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS C 48 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR C 17 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 78 removed outlier: 7.082A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 16 through 20 removed outlier: 6.402A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA D 143 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL D 18 " --> pdb=" O ALA D 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 86 through 94 removed outlier: 5.705A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP D 47 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N THR D 36 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER D 29 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N CYS D 27 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASN D 40 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR D 23 " --> pdb=" O PHE D 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 77 through 78 removed outlier: 3.527A pdb=" N SER D 182 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 77 through 78 removed outlier: 3.527A pdb=" N SER D 182 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 16 through 20 removed outlier: 6.185A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 65 through 66 removed outlier: 4.571A pdb=" N ILE E 92 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU E 26 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE E 42 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU E 24 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N SER E 44 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILE E 22 " --> pdb=" O SER E 44 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 77 through 78 removed outlier: 7.108A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'A' and resid 16 through 20 Processing sheet with id=AB4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.775A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 103 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 43 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 41 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 108 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N THR A 36 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A 29 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LYS A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N CYS A 27 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASN A 40 " --> pdb=" O ILE A 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.865A pdb=" N VAL A 132 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER A 182 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LYS A 183 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL A 169 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 65 removed outlier: 5.105A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 45 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 37 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR B 36 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER B 29 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS B 48 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR B 17 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ALA B 143 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 64 through 65 removed outlier: 5.105A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 45 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 37 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR B 36 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER B 29 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS B 48 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR B 17 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.598A pdb=" N VAL B 132 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B 182 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 10.639A pdb=" N ARG B 179 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N ASN B 173 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 10.456A pdb=" N GLU B 181 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N LYS B 183 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL B 169 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1896 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: 1.98 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2070 1.32 - 1.44: 3627 1.44 - 1.56: 7428 1.56 - 1.68: 8 1.68 - 1.80: 35 Bond restraints: 13168 Sorted by residual: bond pdb=" C ASP A 55 " pdb=" N PRO A 56 " ideal model delta sigma weight residual 1.334 1.344 -0.010 8.40e-03 1.42e+04 1.42e+00 bond pdb=" CA VAL A 79 " pdb=" CB VAL A 79 " ideal model delta sigma weight residual 1.545 1.537 0.008 9.10e-03 1.21e+04 8.24e-01 bond pdb=" CB PHE E 312 " pdb=" CG PHE E 312 " ideal model delta sigma weight residual 1.502 1.520 -0.018 2.30e-02 1.89e+03 6.06e-01 bond pdb=" CB MET C 261 " pdb=" CG MET C 261 " ideal model delta sigma weight residual 1.520 1.497 0.023 3.00e-02 1.11e+03 6.06e-01 bond pdb=" CB ASP C 115 " pdb=" CG ASP C 115 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 6.06e-01 ... (remaining 13163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 17847 2.46 - 4.93: 107 4.93 - 7.39: 10 7.39 - 9.86: 2 9.86 - 12.32: 1 Bond angle restraints: 17967 Sorted by residual: angle pdb=" CA LEU C 246 " pdb=" CB LEU C 246 " pdb=" CG LEU C 246 " ideal model delta sigma weight residual 116.30 128.62 -12.32 3.50e+00 8.16e-02 1.24e+01 angle pdb=" CB LEU C 241 " pdb=" CG LEU C 241 " pdb=" CD2 LEU C 241 " ideal model delta sigma weight residual 110.70 103.11 7.59 3.00e+00 1.11e-01 6.41e+00 angle pdb=" N ALA C 175 " pdb=" CA ALA C 175 " pdb=" C ALA C 175 " ideal model delta sigma weight residual 109.15 112.38 -3.23 1.44e+00 4.82e-01 5.04e+00 angle pdb=" CA TYR E 102 " pdb=" CB TYR E 102 " pdb=" CG TYR E 102 " ideal model delta sigma weight residual 113.90 117.57 -3.67 1.80e+00 3.09e-01 4.17e+00 angle pdb=" C GLU E 243 " pdb=" N THR E 244 " pdb=" CA THR E 244 " ideal model delta sigma weight residual 121.54 117.69 3.85 1.91e+00 2.74e-01 4.07e+00 ... (remaining 17962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.26: 7518 31.26 - 62.52: 303 62.52 - 93.78: 17 93.78 - 125.04: 2 125.04 - 156.30: 5 Dihedral angle restraints: 7845 sinusoidal: 3153 harmonic: 4692 Sorted by residual: dihedral pdb=" CA ARG C 118 " pdb=" C ARG C 118 " pdb=" N TYR C 119 " pdb=" CA TYR C 119 " ideal model delta harmonic sigma weight residual 180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" C3 PEE E 401 " pdb=" C1 PEE E 401 " pdb=" C2 PEE E 401 " pdb=" O3P PEE E 401 " ideal model delta sinusoidal sigma weight residual 62.73 -140.97 -156.30 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" O2 PEE E 401 " pdb=" C1 PEE E 401 " pdb=" C2 PEE E 401 " pdb=" O3P PEE E 401 " ideal model delta sinusoidal sigma weight residual -59.96 93.30 -153.26 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 7842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1544 0.043 - 0.086: 380 0.086 - 0.129: 152 0.129 - 0.172: 5 0.172 - 0.215: 1 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CG LEU C 241 " pdb=" CB LEU C 241 " pdb=" CD1 LEU C 241 " pdb=" CD2 LEU C 241 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE D 240 " pdb=" N ILE D 240 " pdb=" C ILE D 240 " pdb=" CB ILE D 240 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ILE E 73 " pdb=" N ILE E 73 " pdb=" C ILE E 73 " pdb=" CB ILE E 73 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 2079 not shown) Planarity restraints: 2242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 249 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 250 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 250 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 250 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 249 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO C 250 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 250 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 250 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 246 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO B 247 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " -0.024 5.00e-02 4.00e+02 ... (remaining 2239 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1835 2.76 - 3.29: 11659 3.29 - 3.83: 20129 3.83 - 4.36: 22717 4.36 - 4.90: 41586 Nonbonded interactions: 97926 Sorted by model distance: nonbonded pdb=" OG SER E 95 " pdb=" OG1 THR E 99 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR C 119 " pdb=" OH TYR C 197 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR B 102 " pdb=" OE1 GLU B 104 " model vdw 2.230 3.040 nonbonded pdb=" OD1 ASP D 136 " pdb=" NH1 ARG D 179 " model vdw 2.263 3.120 nonbonded pdb=" O PRO E 9 " pdb=" NH1 ARG E 50 " model vdw 2.268 3.120 ... (remaining 97921 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=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.630 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13168 Z= 0.145 Angle : 0.532 12.324 17967 Z= 0.272 Chirality : 0.042 0.215 2082 Planarity : 0.004 0.053 2242 Dihedral : 16.429 156.305 4789 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.43 % Allowed : 18.53 % Favored : 81.04 % 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: 0.40 (0.22), residues: 1559 helix: 3.20 (0.21), residues: 496 sheet: -0.41 (0.28), residues: 387 loop : -1.66 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 293 TYR 0.014 0.001 TYR A 254 PHE 0.010 0.001 PHE C 312 TRP 0.027 0.001 TRP E 72 HIS 0.003 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00340 (13168) covalent geometry : angle 0.53195 (17967) hydrogen bonds : bond 0.19564 ( 589) hydrogen bonds : angle 7.24988 ( 1896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 159 time to evaluate : 0.459 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 163 average time/residue: 0.1202 time to fit residues: 28.1812 Evaluate side-chains 157 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain E residue 18 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.151013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.114764 restraints weight = 46030.325| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 5.57 r_work: 0.2763 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13168 Z= 0.173 Angle : 0.590 16.704 17967 Z= 0.306 Chirality : 0.044 0.158 2082 Planarity : 0.005 0.060 2242 Dihedral : 11.581 153.472 1855 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.35 % Allowed : 17.89 % Favored : 79.76 % 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: 0.46 (0.22), residues: 1559 helix: 3.08 (0.21), residues: 506 sheet: -0.34 (0.26), residues: 423 loop : -1.63 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 179 TYR 0.019 0.001 TYR E 102 PHE 0.013 0.001 PHE C 37 TRP 0.013 0.001 TRP E 72 HIS 0.002 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00418 (13168) covalent geometry : angle 0.59048 (17967) hydrogen bonds : bond 0.07089 ( 589) hydrogen bonds : angle 5.05395 ( 1896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.509 Fit side-chains REVERT: D 88 ASP cc_start: 0.8684 (p0) cc_final: 0.8457 (p0) REVERT: B 26 GLU cc_start: 0.7666 (pt0) cc_final: 0.7356 (pt0) outliers start: 32 outliers final: 22 residues processed: 190 average time/residue: 0.1119 time to fit residues: 31.4579 Evaluate side-chains 184 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 304 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 0.0020 chunk 95 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 109 optimal weight: 0.4980 chunk 66 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.152196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.112216 restraints weight = 48534.788| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.79 r_work: 0.2877 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13168 Z= 0.124 Angle : 0.544 16.375 17967 Z= 0.280 Chirality : 0.043 0.171 2082 Planarity : 0.004 0.050 2242 Dihedral : 11.380 151.543 1852 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.92 % Allowed : 19.03 % Favored : 79.04 % 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: 0.68 (0.22), residues: 1559 helix: 3.30 (0.21), residues: 506 sheet: -0.19 (0.25), residues: 426 loop : -1.56 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 293 TYR 0.013 0.001 TYR D 102 PHE 0.013 0.001 PHE C 37 TRP 0.011 0.001 TRP E 47 HIS 0.002 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00281 (13168) covalent geometry : angle 0.54383 (17967) hydrogen bonds : bond 0.05843 ( 589) hydrogen bonds : angle 4.52231 ( 1896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.483 Fit side-chains REVERT: C 177 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.4402 (mm-30) REVERT: C 187 GLN cc_start: 0.8743 (mt0) cc_final: 0.8451 (mt0) REVERT: E 75 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7006 (pm20) REVERT: B 26 GLU cc_start: 0.7635 (pt0) cc_final: 0.7253 (pt0) REVERT: B 152 ASN cc_start: 0.7616 (t0) cc_final: 0.7324 (t0) outliers start: 26 outliers final: 18 residues processed: 186 average time/residue: 0.1074 time to fit residues: 29.7923 Evaluate side-chains 181 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 69 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 235 HIS A 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.147519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.110582 restraints weight = 44942.887| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 5.08 r_work: 0.2721 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13168 Z= 0.277 Angle : 0.662 15.863 17967 Z= 0.343 Chirality : 0.047 0.176 2082 Planarity : 0.005 0.065 2242 Dihedral : 11.653 153.338 1852 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.64 % Allowed : 17.68 % Favored : 78.69 % 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: 0.32 (0.21), residues: 1559 helix: 2.79 (0.21), residues: 503 sheet: -0.10 (0.25), residues: 421 loop : -1.80 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 293 TYR 0.020 0.002 TYR E 102 PHE 0.021 0.002 PHE C 37 TRP 0.012 0.002 TRP E 47 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00701 (13168) covalent geometry : angle 0.66176 (17967) hydrogen bonds : bond 0.08470 ( 589) hydrogen bonds : angle 4.84274 ( 1896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 159 time to evaluate : 0.480 Fit side-chains REVERT: C 177 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.4373 (mm-30) REVERT: D 157 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7946 (tt) REVERT: B 26 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7278 (pt0) REVERT: B 152 ASN cc_start: 0.7490 (t0) cc_final: 0.7124 (t0) outliers start: 50 outliers final: 39 residues processed: 192 average time/residue: 0.1110 time to fit residues: 31.9267 Evaluate side-chains 198 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 304 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 63 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN A 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.150524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.110228 restraints weight = 46928.279| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.69 r_work: 0.2868 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13168 Z= 0.120 Angle : 0.546 15.721 17967 Z= 0.282 Chirality : 0.043 0.172 2082 Planarity : 0.004 0.045 2242 Dihedral : 11.319 153.441 1852 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.42 % Allowed : 19.03 % Favored : 78.55 % 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: 0.70 (0.22), residues: 1559 helix: 3.23 (0.21), residues: 506 sheet: 0.02 (0.25), residues: 422 loop : -1.64 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 293 TYR 0.014 0.001 TYR D 102 PHE 0.017 0.001 PHE C 37 TRP 0.013 0.001 TRP E 47 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00269 (13168) covalent geometry : angle 0.54630 (17967) hydrogen bonds : bond 0.05774 ( 589) hydrogen bonds : angle 4.34421 ( 1896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.472 Fit side-chains REVERT: C 177 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.4328 (mm-30) REVERT: C 187 GLN cc_start: 0.8729 (mt0) cc_final: 0.8474 (mt0) REVERT: D 26 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7878 (pm20) REVERT: D 157 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7906 (tt) REVERT: E 75 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.6997 (pm20) REVERT: A 102 TYR cc_start: 0.8343 (t80) cc_final: 0.7761 (t80) REVERT: B 26 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7260 (pt0) outliers start: 33 outliers final: 22 residues processed: 192 average time/residue: 0.1135 time to fit residues: 32.2911 Evaluate side-chains 190 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 126 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN A 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.149684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.108670 restraints weight = 43693.994| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.61 r_work: 0.2900 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13168 Z= 0.143 Angle : 0.556 15.663 17967 Z= 0.285 Chirality : 0.043 0.233 2082 Planarity : 0.005 0.063 2242 Dihedral : 11.236 153.732 1852 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.92 % Allowed : 18.75 % Favored : 78.33 % 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: 0.74 (0.22), residues: 1559 helix: 3.24 (0.21), residues: 506 sheet: 0.05 (0.25), residues: 424 loop : -1.59 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 293 TYR 0.013 0.001 TYR E 102 PHE 0.018 0.001 PHE C 37 TRP 0.013 0.001 TRP E 47 HIS 0.002 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00342 (13168) covalent geometry : angle 0.55612 (17967) hydrogen bonds : bond 0.06073 ( 589) hydrogen bonds : angle 4.31986 ( 1896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.521 Fit side-chains REVERT: C 177 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.4463 (mm-30) REVERT: C 187 GLN cc_start: 0.8700 (mt0) cc_final: 0.8436 (mt0) REVERT: D 26 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: D 157 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7923 (tt) REVERT: E 75 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.6977 (pm20) REVERT: A 102 TYR cc_start: 0.8300 (t80) cc_final: 0.7691 (t80) REVERT: B 26 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7249 (pt0) REVERT: B 152 ASN cc_start: 0.7669 (t0) cc_final: 0.7368 (t0) outliers start: 40 outliers final: 34 residues processed: 192 average time/residue: 0.1155 time to fit residues: 33.0678 Evaluate side-chains 200 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 7 optimal weight: 0.0030 chunk 74 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN A 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.159193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.122183 restraints weight = 37624.947| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 4.22 r_work: 0.2912 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13168 Z= 0.108 Angle : 0.528 15.420 17967 Z= 0.270 Chirality : 0.042 0.185 2082 Planarity : 0.004 0.050 2242 Dihedral : 10.922 153.928 1852 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.49 % Allowed : 19.10 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.22), residues: 1559 helix: 3.37 (0.21), residues: 506 sheet: 0.16 (0.25), residues: 422 loop : -1.52 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 293 TYR 0.012 0.001 TYR C 102 PHE 0.014 0.001 PHE C 37 TRP 0.013 0.001 TRP E 72 HIS 0.002 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00236 (13168) covalent geometry : angle 0.52828 (17967) hydrogen bonds : bond 0.04837 ( 589) hydrogen bonds : angle 4.07513 ( 1896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: C 177 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.4504 (mm-30) REVERT: C 187 GLN cc_start: 0.8680 (mt0) cc_final: 0.8416 (mt0) REVERT: D 25 ILE cc_start: 0.9102 (mt) cc_final: 0.8543 (mt) REVERT: D 26 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: D 157 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7840 (tt) REVERT: E 75 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: A 102 TYR cc_start: 0.8288 (t80) cc_final: 0.7716 (t80) REVERT: A 313 LEU cc_start: 0.8320 (tt) cc_final: 0.8011 (tp) REVERT: B 26 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7303 (pt0) REVERT: B 152 ASN cc_start: 0.7706 (t0) cc_final: 0.7493 (t0) outliers start: 34 outliers final: 25 residues processed: 196 average time/residue: 0.1038 time to fit residues: 30.5197 Evaluate side-chains 200 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 11 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 134 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.158255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.121981 restraints weight = 43054.009| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 5.07 r_work: 0.2837 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13168 Z= 0.119 Angle : 0.534 15.140 17967 Z= 0.271 Chirality : 0.043 0.206 2082 Planarity : 0.004 0.055 2242 Dihedral : 10.835 154.352 1852 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.57 % Allowed : 19.03 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.22), residues: 1559 helix: 3.36 (0.21), residues: 506 sheet: 0.19 (0.25), residues: 424 loop : -1.47 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 293 TYR 0.012 0.001 TYR E 102 PHE 0.015 0.001 PHE C 37 TRP 0.021 0.001 TRP E 72 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00276 (13168) covalent geometry : angle 0.53430 (17967) hydrogen bonds : bond 0.05169 ( 589) hydrogen bonds : angle 4.07186 ( 1896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.512 Fit side-chains REVERT: C 177 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.4505 (mm-30) REVERT: C 187 GLN cc_start: 0.8687 (mt0) cc_final: 0.8441 (mt0) REVERT: D 25 ILE cc_start: 0.9086 (mt) cc_final: 0.8531 (mt) REVERT: D 26 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8054 (pm20) REVERT: D 157 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7817 (tt) REVERT: E 75 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6804 (pm20) REVERT: A 102 TYR cc_start: 0.8270 (t80) cc_final: 0.7704 (t80) REVERT: B 26 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7388 (pt0) REVERT: B 152 ASN cc_start: 0.7621 (t0) cc_final: 0.7388 (t0) outliers start: 35 outliers final: 25 residues processed: 193 average time/residue: 0.1093 time to fit residues: 31.4651 Evaluate side-chains 201 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 264 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.146428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.109641 restraints weight = 41722.512| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 5.27 r_work: 0.2734 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 13168 Z= 0.267 Angle : 0.661 14.872 17967 Z= 0.341 Chirality : 0.046 0.250 2082 Planarity : 0.005 0.062 2242 Dihedral : 11.346 156.223 1852 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.49 % Allowed : 19.39 % Favored : 78.12 % 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: 0.48 (0.21), residues: 1559 helix: 2.88 (0.21), residues: 503 sheet: 0.08 (0.25), residues: 422 loop : -1.73 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 293 TYR 0.019 0.002 TYR E 102 PHE 0.022 0.002 PHE C 37 TRP 0.029 0.002 TRP E 72 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00669 (13168) covalent geometry : angle 0.66147 (17967) hydrogen bonds : bond 0.08185 ( 589) hydrogen bonds : angle 4.61061 ( 1896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.577 Fit side-chains REVERT: C 177 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.4448 (mm-30) REVERT: C 187 GLN cc_start: 0.8721 (mt0) cc_final: 0.8467 (mt0) REVERT: D 26 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8074 (pm20) REVERT: D 157 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7955 (tt) REVERT: B 26 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7349 (pt0) outliers start: 34 outliers final: 27 residues processed: 190 average time/residue: 0.1095 time to fit residues: 31.2019 Evaluate side-chains 196 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 304 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 137 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 107 optimal weight: 0.0770 chunk 104 optimal weight: 0.0010 chunk 73 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 0.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 ASN A 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.153288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.113510 restraints weight = 52717.890| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 4.07 r_work: 0.2883 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13168 Z= 0.108 Angle : 0.557 15.191 17967 Z= 0.283 Chirality : 0.043 0.199 2082 Planarity : 0.004 0.047 2242 Dihedral : 10.829 154.910 1852 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.14 % Allowed : 20.03 % Favored : 77.83 % 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 (0.22), residues: 1559 helix: 3.32 (0.21), residues: 506 sheet: 0.18 (0.25), residues: 422 loop : -1.51 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 293 TYR 0.016 0.001 TYR C 102 PHE 0.011 0.001 PHE A 42 TRP 0.038 0.001 TRP E 72 HIS 0.002 0.001 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00229 (13168) covalent geometry : angle 0.55719 (17967) hydrogen bonds : bond 0.04915 ( 589) hydrogen bonds : angle 4.07818 ( 1896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.632 Fit side-chains REVERT: C 177 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.4456 (mm-30) REVERT: C 187 GLN cc_start: 0.8661 (mt0) cc_final: 0.8399 (mt0) REVERT: D 25 ILE cc_start: 0.9016 (mt) cc_final: 0.8428 (mt) REVERT: D 26 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: A 102 TYR cc_start: 0.8257 (t80) cc_final: 0.7694 (t80) REVERT: A 313 LEU cc_start: 0.8268 (tt) cc_final: 0.8060 (tp) REVERT: B 26 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7252 (pt0) outliers start: 29 outliers final: 24 residues processed: 195 average time/residue: 0.1124 time to fit residues: 32.7463 Evaluate side-chains 192 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 123 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 98 optimal weight: 0.0040 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.155127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.118577 restraints weight = 39416.251| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 4.78 r_work: 0.2847 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13168 Z= 0.112 Angle : 0.551 14.861 17967 Z= 0.275 Chirality : 0.042 0.158 2082 Planarity : 0.005 0.107 2242 Dihedral : 10.681 155.011 1852 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.85 % Allowed : 20.38 % Favored : 77.76 % 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 (0.22), residues: 1559 helix: 3.35 (0.21), residues: 506 sheet: 0.23 (0.26), residues: 422 loop : -1.45 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 293 TYR 0.016 0.001 TYR C 102 PHE 0.015 0.001 PHE C 37 TRP 0.036 0.001 TRP E 72 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00250 (13168) covalent geometry : angle 0.55064 (17967) hydrogen bonds : bond 0.04939 ( 589) hydrogen bonds : angle 4.01762 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3125.61 seconds wall clock time: 54 minutes 14.92 seconds (3254.92 seconds total)