Starting phenix.real_space_refine on Sun Nov 17 10:41:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i47_35163/11_2024/8i47_35163.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i47_35163/11_2024/8i47_35163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i47_35163/11_2024/8i47_35163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i47_35163/11_2024/8i47_35163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i47_35163/11_2024/8i47_35163.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i47_35163/11_2024/8i47_35163.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.049 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 30 5.49 5 S 20 5.16 5 C 9050 2.51 5 N 2055 2.21 5 O 2540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13695 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "B" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "D" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "E" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "C" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 232 Unusual residues: {'PEE': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 133 Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {'PEE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 99 Chain: "D" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {'PEE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 99 Chain: "E" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 196 Unusual residues: {'PEE': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 116 Chain: "C" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 232 Unusual residues: {'PEE': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 133 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 12.99, per 1000 atoms: 0.95 Number of scatterers: 13695 At special positions: 0 Unit cell: (96.3528, 94.6624, 120.018, 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 30 15.00 O 2540 8.00 N 2055 7.00 C 9050 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: 3.05 Conformation dependent library (CDL) restraints added in 3.0 seconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 40.2% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 196 through 213 removed outlier: 5.352A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 220 through 243 Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.672A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 196 through 213 removed outlier: 5.353A pdb=" N LEU B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 220 through 243 Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 284 through 315 removed outlier: 3.670A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'D' and resid 58 through 62 Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'D' and resid 196 through 213 removed outlier: 5.353A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Proline residue: D 204 - end of helix Processing helix chain 'D' and resid 214 through 218 Processing helix chain 'D' and resid 220 through 243 Processing helix chain 'D' and resid 253 through 282 Processing helix chain 'D' and resid 284 through 315 removed outlier: 3.670A pdb=" N ILE D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 176 through 180 Processing helix chain 'E' and resid 196 through 213 removed outlier: 5.353A pdb=" N LEU E 203 " --> pdb=" O PRO E 199 " (cutoff:3.500A) Proline residue: E 204 - end of helix Processing helix chain 'E' and resid 214 through 218 Processing helix chain 'E' and resid 220 through 243 Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 253 through 282 Processing helix chain 'E' and resid 284 through 315 removed outlier: 3.677A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 196 through 213 removed outlier: 5.353A 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 Processing helix chain 'C' and resid 220 through 243 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 284 through 315 removed outlier: 3.669A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 94 removed outlier: 5.581A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 100 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP A 47 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LYS A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N CYS A 27 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN A 40 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 19 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.580A pdb=" N LYS A 183 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL A 169 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 89 through 94 removed outlier: 5.581A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 100 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP B 47 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 19 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.580A pdb=" N LYS B 183 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL B 169 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 89 through 94 removed outlier: 5.583A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 100 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP D 47 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LYS D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N CYS D 27 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN D 40 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 19 " --> pdb=" O SER D 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.580A pdb=" N LYS D 183 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL D 169 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 89 through 94 removed outlier: 5.581A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 100 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP E 47 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN E 19 " --> pdb=" O SER E 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.580A pdb=" N LYS E 183 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL E 169 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 89 through 94 removed outlier: 5.581A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 100 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP C 47 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LYS C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N CYS C 27 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN C 40 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 19 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.580A pdb=" N LYS C 183 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL C 169 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1735 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: 3.69 Time building geometry restraints manager: 3.55 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: 2189 1.32 - 1.44: 3706 1.44 - 1.57: 7990 1.57 - 1.69: 60 1.69 - 1.81: 35 Bond restraints: 13980 Sorted by residual: bond pdb=" N LYS B 148 " pdb=" CA LYS B 148 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 9.94e+00 bond pdb=" N LYS C 148 " pdb=" CA LYS C 148 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.80e+00 bond pdb=" N LYS A 148 " pdb=" CA LYS A 148 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.43e+00 bond pdb=" N LYS D 148 " pdb=" CA LYS D 148 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.32e+00 bond pdb=" N LYS E 148 " pdb=" CA LYS E 148 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.22e+00 ... (remaining 13975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 16984 1.23 - 2.47: 1536 2.47 - 3.70: 261 3.70 - 4.93: 89 4.93 - 6.16: 45 Bond angle restraints: 18915 Sorted by residual: angle pdb=" CA GLU C 147 " pdb=" C GLU C 147 " pdb=" N LYS C 148 " ideal model delta sigma weight residual 115.29 120.59 -5.30 1.44e+00 4.82e-01 1.36e+01 angle pdb=" CA GLU A 147 " pdb=" C GLU A 147 " pdb=" N LYS A 148 " ideal model delta sigma weight residual 115.29 120.57 -5.28 1.44e+00 4.82e-01 1.34e+01 angle pdb=" CA GLU D 147 " pdb=" C GLU D 147 " pdb=" N LYS D 148 " ideal model delta sigma weight residual 115.29 120.56 -5.27 1.44e+00 4.82e-01 1.34e+01 angle pdb=" CA GLU E 147 " pdb=" C GLU E 147 " pdb=" N LYS E 148 " ideal model delta sigma weight residual 115.29 120.55 -5.26 1.44e+00 4.82e-01 1.34e+01 angle pdb=" CA GLU B 147 " pdb=" C GLU B 147 " pdb=" N LYS B 148 " ideal model delta sigma weight residual 115.29 120.50 -5.21 1.44e+00 4.82e-01 1.31e+01 ... (remaining 18910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.39: 7878 27.39 - 54.77: 507 54.77 - 82.16: 60 82.16 - 109.55: 75 109.55 - 136.93: 20 Dihedral angle restraints: 8540 sinusoidal: 3840 harmonic: 4700 Sorted by residual: dihedral pdb=" C4 PEE C 407 " pdb=" O4P PEE C 407 " pdb=" P PEE C 407 " pdb=" O2P PEE C 407 " ideal model delta sinusoidal sigma weight residual -75.78 61.15 -136.93 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C4 PEE E 406 " pdb=" O4P PEE E 406 " pdb=" P PEE E 406 " pdb=" O2P PEE E 406 " ideal model delta sinusoidal sigma weight residual -75.78 61.14 -136.92 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C4 PEE A 405 " pdb=" O4P PEE A 405 " pdb=" P PEE A 405 " pdb=" O2P PEE A 405 " ideal model delta sinusoidal sigma weight residual -75.78 61.14 -136.92 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 8537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1153 0.035 - 0.069: 624 0.069 - 0.104: 243 0.104 - 0.139: 75 0.139 - 0.173: 15 Chirality restraints: 2110 Sorted by residual: chirality pdb=" CG LEU D 146 " pdb=" CB LEU D 146 " pdb=" CD1 LEU D 146 " pdb=" CD2 LEU D 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CG LEU E 146 " pdb=" CB LEU E 146 " pdb=" CD1 LEU E 146 " pdb=" CD2 LEU E 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CG LEU B 146 " pdb=" CB LEU B 146 " pdb=" CD1 LEU B 146 " pdb=" CD2 LEU B 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.35e-01 ... (remaining 2107 not shown) Planarity restraints: 2295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 312 " -0.012 2.00e-02 2.50e+03 5.89e-02 6.07e+01 pdb=" CG PHE D 312 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 PHE D 312 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 PHE D 312 " -0.086 2.00e-02 2.50e+03 pdb=" CE1 PHE D 312 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE D 312 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE D 312 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 312 " -0.012 2.00e-02 2.50e+03 5.89e-02 6.07e+01 pdb=" CG PHE B 312 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 PHE B 312 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 PHE B 312 " -0.086 2.00e-02 2.50e+03 pdb=" CE1 PHE B 312 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE B 312 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE B 312 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 312 " -0.012 2.00e-02 2.50e+03 5.88e-02 6.05e+01 pdb=" CG PHE E 312 " 0.115 2.00e-02 2.50e+03 pdb=" CD1 PHE E 312 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 PHE E 312 " -0.086 2.00e-02 2.50e+03 pdb=" CE1 PHE E 312 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE E 312 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE E 312 " 0.024 2.00e-02 2.50e+03 ... (remaining 2292 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 783 2.73 - 3.27: 13212 3.27 - 3.81: 21432 3.81 - 4.36: 26948 4.36 - 4.90: 45686 Nonbonded interactions: 108061 Sorted by model distance: nonbonded pdb=" N GLU E 82 " pdb=" OE1 GLU E 82 " model vdw 2.184 3.120 nonbonded pdb=" N GLU A 82 " pdb=" OE1 GLU A 82 " model vdw 2.184 3.120 nonbonded pdb=" N GLU C 82 " pdb=" OE1 GLU C 82 " model vdw 2.184 3.120 nonbonded pdb=" N GLU D 82 " pdb=" OE1 GLU D 82 " model vdw 2.184 3.120 nonbonded pdb=" N GLU B 82 " pdb=" OE1 GLU B 82 " model vdw 2.185 3.120 ... (remaining 108056 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 or (resid 401 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name O1P or name O2 or name O2P or name O3 or name O3P or name \ O4 or name O4P or name O5 or name P )) or (resid 402 and (name C1 or name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 \ or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name O1P or name O2 or name O2P or name O3 or nam \ e O3P or name O4 or name O4P or name O5 or name P )) or (resid 403 and (name C1 \ or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or nam \ e C35 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or na \ me O4P or name O5 or name P )) or (resid 404 and (name C1 or name C10 or name C1 \ 1 or name C12 or name C13 or name C2 or name C3 or name C30 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name O1P or name O2 or name O2P or na \ me O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 405 a \ nd (name C1 or name C10 or name C11 or name C12 or name C13 or name O1P or name \ O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name \ P )))) selection = (chain 'B' and (resid 5 through 292 or resid 294 through 316 or resid 401 or (re \ sid 402 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C2 or name C3 or name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O1P or na \ me O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or na \ me P )) or (resid 403 and (name C1 or name C10 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C3 or name C30 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name O1P or name O2 or name O2P or n \ ame O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 404 \ and (name C1 or name C10 or name C11 or name C12 or name C13 or name C2 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or na \ me O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or n \ ame O5 or name P )) or (resid 405 and (name C1 or name C10 or name C11 or name C \ 12 or name C13 or name O1P or name O2 or name O2P or name O3 or name O3P or name \ O4 or name O4P or name O5 or name P )))) selection = (chain 'C' and (resid 5 through 292 or resid 294 through 316 or resid 401 or (re \ sid 402 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C2 or name C3 or name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O1P or na \ me O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or na \ me P )) or (resid 403 and (name C1 or name C10 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C3 or name C30 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name O1P or name O2 or name O2P or n \ ame O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 404 \ and (name C1 or name C10 or name C11 or name C12 or name C13 or name C2 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or na \ me O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or n \ ame O5 or name P )) or (resid 405 and (name C1 or name C10 or name C11 or name C \ 12 or name C13 or name O1P or name O2 or name O2P or name O3 or name O3P or name \ O4 or name O4P or name O5 or name P )))) selection = (chain 'D' and (resid 5 through 292 or resid 294 through 316 or (resid 401 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name O1P or name O2 or name O2P or name O3 or name O3P or name \ O4 or name O4P or name O5 or name P )) or (resid 402 and (name C1 or name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 \ or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name O1P or name O2 or name O2P or name O3 or nam \ e O3P or name O4 or name O4P or name O5 or name P )) or (resid 403 and (name C1 \ or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or nam \ e C35 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or na \ me O4P or name O5 or name P )) or (resid 404 and (name C1 or name C10 or name C1 \ 1 or name C12 or name C13 or name C2 or name C3 or name C30 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name O1P or name O2 or name O2P or na \ me O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 405 a \ nd (name C1 or name C10 or name C11 or name C12 or name C13 or name O1P or name \ O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name \ P )))) selection = (chain 'E' and (resid 5 through 292 or resid 294 through 316 or resid 401 or (re \ sid 402 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C2 or name C3 or name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O1P or na \ me O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or na \ me P )) or (resid 403 and (name C1 or name C10 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C3 or name C30 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name O1P or name O2 or name O2P or n \ ame O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 404 \ and (name C1 or name C10 or name C11 or name C12 or name C13 or name C2 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or na \ me O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or n \ ame O5 or name P )) or (resid 405 and (name C1 or name C10 or name C11 or name C \ 12 or name C13 or name O1P or name O2 or name O2P or name O3 or name O3P or name \ O4 or name O4P or name O5 or name P )))) } 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=0.42 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: 0.700 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.400 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.004 0.041 13980 Z= 0.282 Angle : 0.840 6.164 18915 Z= 0.461 Chirality : 0.049 0.173 2110 Planarity : 0.014 0.125 2295 Dihedral : 21.441 136.934 5480 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.00 % Allowed : 21.14 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.20), residues: 1555 helix: 0.21 (0.20), residues: 555 sheet: -1.51 (0.23), residues: 445 loop : -2.39 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.008 TRP E 217 HIS 0.004 0.002 HIS C 277 PHE 0.116 0.009 PHE D 312 TYR 0.026 0.005 TYR B 221 ARG 0.021 0.002 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.362 Fit side-chains REVERT: A 252 MET cc_start: 0.8108 (tpt) cc_final: 0.7760 (mmm) REVERT: B 44 SER cc_start: 0.7220 (t) cc_final: 0.6933 (p) REVERT: B 252 MET cc_start: 0.8018 (tpt) cc_final: 0.7739 (mmm) REVERT: D 252 MET cc_start: 0.8134 (tpt) cc_final: 0.7761 (mmm) REVERT: E 252 MET cc_start: 0.8071 (tpt) cc_final: 0.7782 (mmm) outliers start: 14 outliers final: 8 residues processed: 110 average time/residue: 1.0043 time to fit residues: 125.0031 Evaluate side-chains 100 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 62 optimal weight: 60.0000 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 0.0770 chunk 90 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 13980 Z= 0.457 Angle : 0.756 7.305 18915 Z= 0.394 Chirality : 0.051 0.197 2110 Planarity : 0.006 0.045 2295 Dihedral : 21.824 134.568 2544 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.28 % Allowed : 19.07 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1555 helix: 1.92 (0.21), residues: 525 sheet: -0.87 (0.24), residues: 415 loop : -1.63 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 213 HIS 0.005 0.003 HIS C 235 PHE 0.020 0.003 PHE B 207 TYR 0.017 0.003 TYR E 186 ARG 0.004 0.001 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 TYR cc_start: 0.8131 (m-10) cc_final: 0.7909 (m-80) REVERT: B 252 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7765 (mmm) REVERT: E 86 ASP cc_start: 0.7400 (t0) cc_final: 0.7152 (t0) outliers start: 32 outliers final: 20 residues processed: 115 average time/residue: 0.9133 time to fit residues: 120.4405 Evaluate side-chains 110 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 141 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13980 Z= 0.210 Angle : 0.596 6.104 18915 Z= 0.308 Chirality : 0.044 0.140 2110 Planarity : 0.005 0.045 2295 Dihedral : 20.047 138.608 2543 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.99 % Allowed : 18.93 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1555 helix: 2.69 (0.21), residues: 525 sheet: -0.65 (0.23), residues: 420 loop : -1.36 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 72 HIS 0.003 0.001 HIS A 277 PHE 0.011 0.001 PHE C 37 TYR 0.011 0.001 TYR A 186 ARG 0.003 0.000 ARG E 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.6125 (m-40) cc_final: 0.5757 (p0) REVERT: B 109 ARG cc_start: 0.7961 (mtp85) cc_final: 0.7722 (mtt-85) REVERT: E 19 ASN cc_start: 0.6201 (m-40) cc_final: 0.5661 (p0) REVERT: E 86 ASP cc_start: 0.7335 (t0) cc_final: 0.6988 (t0) outliers start: 28 outliers final: 18 residues processed: 133 average time/residue: 1.0113 time to fit residues: 151.3762 Evaluate side-chains 116 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 0.1980 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 141 optimal weight: 0.0170 chunk 149 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 0.0050 chunk 124 optimal weight: 60.0000 overall best weight: 1.0436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 187 GLN C 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13980 Z= 0.179 Angle : 0.570 5.968 18915 Z= 0.293 Chirality : 0.043 0.130 2110 Planarity : 0.004 0.043 2295 Dihedral : 18.890 144.364 2539 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.71 % Allowed : 19.72 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1555 helix: 2.94 (0.21), residues: 525 sheet: -0.38 (0.23), residues: 425 loop : -1.12 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 72 HIS 0.002 0.001 HIS A 277 PHE 0.011 0.001 PHE B 37 TYR 0.008 0.001 TYR C 186 ARG 0.003 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ASN cc_start: 0.6184 (m-40) cc_final: 0.5795 (p0) REVERT: B 86 ASP cc_start: 0.7202 (t0) cc_final: 0.6932 (t0) REVERT: E 19 ASN cc_start: 0.5732 (m-40) cc_final: 0.5290 (p0) REVERT: E 86 ASP cc_start: 0.7387 (t0) cc_final: 0.6997 (t0) outliers start: 24 outliers final: 10 residues processed: 124 average time/residue: 1.0835 time to fit residues: 151.6282 Evaluate side-chains 111 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 128 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 0 optimal weight: 60.0000 chunk 76 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13980 Z= 0.175 Angle : 0.555 5.968 18915 Z= 0.284 Chirality : 0.042 0.129 2110 Planarity : 0.004 0.041 2295 Dihedral : 18.381 149.528 2539 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.35 % Allowed : 20.64 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.21), residues: 1555 helix: 3.00 (0.21), residues: 525 sheet: -0.16 (0.24), residues: 415 loop : -1.09 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 72 HIS 0.002 0.001 HIS B 277 PHE 0.011 0.001 PHE B 37 TYR 0.008 0.001 TYR A 186 ARG 0.002 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 19 ASN cc_start: 0.6228 (m-40) cc_final: 0.5871 (p0) REVERT: B 86 ASP cc_start: 0.7190 (t0) cc_final: 0.6897 (t0) REVERT: E 19 ASN cc_start: 0.5547 (m-40) cc_final: 0.5146 (p0) REVERT: E 86 ASP cc_start: 0.7408 (t0) cc_final: 0.6916 (t0) REVERT: C 187 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7726 (mt0) outliers start: 19 outliers final: 11 residues processed: 125 average time/residue: 1.0331 time to fit residues: 146.3168 Evaluate side-chains 119 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 187 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 30.0000 chunk 149 optimal weight: 2.9990 chunk 124 optimal weight: 60.0000 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13980 Z= 0.247 Angle : 0.604 6.329 18915 Z= 0.310 Chirality : 0.044 0.130 2110 Planarity : 0.004 0.040 2295 Dihedral : 18.650 147.154 2537 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.70 % Allowed : 19.36 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1555 helix: 2.81 (0.21), residues: 525 sheet: -0.30 (0.23), residues: 440 loop : -1.15 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 160 HIS 0.002 0.001 HIS A 127 PHE 0.013 0.002 PHE A 106 TYR 0.011 0.001 TYR C 186 ARG 0.004 0.000 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ASP cc_start: 0.7169 (t0) cc_final: 0.6840 (t0) REVERT: E 86 ASP cc_start: 0.7344 (t0) cc_final: 0.6846 (t0) outliers start: 38 outliers final: 26 residues processed: 133 average time/residue: 1.0165 time to fit residues: 151.9354 Evaluate side-chains 135 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 252 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 93 optimal weight: 60.0000 chunk 91 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13980 Z= 0.167 Angle : 0.550 5.966 18915 Z= 0.282 Chirality : 0.042 0.130 2110 Planarity : 0.004 0.039 2295 Dihedral : 18.092 150.062 2537 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.49 % Allowed : 20.64 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1555 helix: 3.00 (0.21), residues: 525 sheet: -0.03 (0.24), residues: 415 loop : -1.01 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 160 HIS 0.004 0.001 HIS D 235 PHE 0.010 0.001 PHE B 37 TYR 0.008 0.001 TYR A 263 ARG 0.002 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.331 Fit side-chains REVERT: B 86 ASP cc_start: 0.7081 (t0) cc_final: 0.6750 (t0) REVERT: E 86 ASP cc_start: 0.7387 (t0) cc_final: 0.6931 (t0) outliers start: 21 outliers final: 17 residues processed: 126 average time/residue: 1.0269 time to fit residues: 145.9859 Evaluate side-chains 123 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 94 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13980 Z= 0.171 Angle : 0.555 6.735 18915 Z= 0.283 Chirality : 0.042 0.131 2110 Planarity : 0.004 0.038 2295 Dihedral : 17.697 154.457 2537 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.64 % Allowed : 20.28 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.21), residues: 1555 helix: 3.03 (0.21), residues: 525 sheet: 0.09 (0.24), residues: 410 loop : -1.03 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 160 HIS 0.002 0.001 HIS E 277 PHE 0.011 0.001 PHE D 37 TYR 0.007 0.001 TYR B 251 ARG 0.002 0.000 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.462 Fit side-chains REVERT: B 86 ASP cc_start: 0.7062 (t0) cc_final: 0.6723 (t0) REVERT: E 86 ASP cc_start: 0.7335 (t0) cc_final: 0.6936 (t0) outliers start: 23 outliers final: 18 residues processed: 125 average time/residue: 0.9007 time to fit residues: 128.3362 Evaluate side-chains 127 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 252 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 139 optimal weight: 0.0570 chunk 83 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 0.0870 chunk 42 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13980 Z= 0.149 Angle : 0.532 5.866 18915 Z= 0.271 Chirality : 0.041 0.131 2110 Planarity : 0.004 0.038 2295 Dihedral : 17.182 163.332 2537 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.14 % Allowed : 20.93 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.21), residues: 1555 helix: 3.21 (0.20), residues: 520 sheet: 0.15 (0.24), residues: 410 loop : -1.03 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 213 HIS 0.002 0.001 HIS C 277 PHE 0.010 0.001 PHE E 37 TYR 0.007 0.001 TYR A 263 ARG 0.002 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.501 Fit side-chains REVERT: B 86 ASP cc_start: 0.7073 (t0) cc_final: 0.6743 (t0) REVERT: E 86 ASP cc_start: 0.7292 (t0) cc_final: 0.6950 (t0) REVERT: E 147 GLU cc_start: 0.8353 (tt0) cc_final: 0.8002 (mp0) outliers start: 16 outliers final: 13 residues processed: 126 average time/residue: 0.8730 time to fit residues: 126.4043 Evaluate side-chains 120 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 ASN E 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13980 Z= 0.218 Angle : 0.584 7.310 18915 Z= 0.298 Chirality : 0.043 0.133 2110 Planarity : 0.004 0.038 2295 Dihedral : 17.513 165.393 2537 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.28 % Allowed : 21.21 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1555 helix: 2.94 (0.21), residues: 525 sheet: 0.07 (0.24), residues: 410 loop : -1.04 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 160 HIS 0.002 0.001 HIS B 277 PHE 0.011 0.001 PHE E 106 TYR 0.008 0.001 TYR D 263 ARG 0.002 0.000 ARG C 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.403 Fit side-chains REVERT: B 86 ASP cc_start: 0.7059 (t0) cc_final: 0.6719 (t0) REVERT: E 86 ASP cc_start: 0.7298 (t0) cc_final: 0.6908 (t0) REVERT: E 147 GLU cc_start: 0.8398 (tt0) cc_final: 0.8013 (mp0) outliers start: 18 outliers final: 13 residues processed: 123 average time/residue: 0.8849 time to fit residues: 125.0493 Evaluate side-chains 117 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 113 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 34 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 HIS E 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.225164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.179400 restraints weight = 22977.983| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 3.89 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4060 r_free = 0.4060 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4060 r_free = 0.4060 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 13980 Z= 0.231 Angle : 0.805 59.192 18915 Z= 0.466 Chirality : 0.048 1.054 2110 Planarity : 0.004 0.066 2295 Dihedral : 17.530 165.391 2535 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 1.14 % Allowed : 21.28 % Favored : 77.58 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.21), residues: 1555 helix: 2.90 (0.21), residues: 525 sheet: 0.07 (0.24), residues: 410 loop : -1.04 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 160 HIS 0.002 0.001 HIS B 277 PHE 0.010 0.001 PHE B 37 TYR 0.008 0.001 TYR B 251 ARG 0.002 0.000 ARG C 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3331.96 seconds wall clock time: 61 minutes 15.99 seconds (3675.99 seconds total)