Starting phenix.real_space_refine on Fri Jul 3 09:50:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lak_62931/07_2026/9lak_62931.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lak_62931/07_2026/9lak_62931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lak_62931/07_2026/9lak_62931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lak_62931/07_2026/9lak_62931.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lak_62931/07_2026/9lak_62931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lak_62931/07_2026/9lak_62931.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 S 20 5.16 5 Cl 3 4.86 5 C 8754 2.51 5 N 2027 2.21 5 O 2374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13191 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "D" Number of atoms: 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: 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: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 145 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 5} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 104 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 56 Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 108 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 3.30, per 1000 atoms: 0.25 Number of scatterers: 13191 At special positions: 0 Unit cell: (96.52, 91.96, 129.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 20 16.00 P 13 15.00 O 2374 8.00 N 2027 7.00 C 8754 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: 1.08 Conformation dependent library (CDL) restraints added in 553.8 milliseconds 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 17 sheets defined 39.2% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'C' and resid 50 through 53 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 146 through 149 removed outlier: 3.856A pdb=" N VAL C 149 " --> pdb=" O LEU C 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 146 through 149' Processing helix chain 'C' and resid 196 through 213 removed outlier: 3.557A pdb=" N ASN C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 5.135A 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: 3.520A pdb=" N TRP C 217 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 214 through 218' Processing helix chain 'C' and resid 220 through 244 Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 284 through 316 removed outlier: 3.654A pdb=" N ALA C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 50 through 53 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 146 through 149 removed outlier: 3.730A pdb=" N VAL D 149 " --> pdb=" O LEU D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 196 through 201 removed outlier: 3.616A pdb=" N ASN D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 214 Processing helix chain 'D' and resid 215 through 218 removed outlier: 3.674A pdb=" N SER D 218 " --> pdb=" O ALA D 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 215 through 218' Processing helix chain 'D' and resid 220 through 244 Processing helix chain 'D' and resid 253 through 282 Processing helix chain 'D' and resid 284 through 316 removed outlier: 3.612A pdb=" N ALA D 288 " --> pdb=" O GLN D 284 " (cutoff:3.500A) removed outlier: 3.793A 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 50 through 53 removed outlier: 3.938A 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 146 through 149 removed outlier: 3.614A pdb=" N VAL E 149 " --> pdb=" O LEU E 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 146 through 149' Processing helix chain 'E' and resid 196 through 201 removed outlier: 3.590A pdb=" N ASN E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 214 removed outlier: 3.558A pdb=" N MET E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 218 removed outlier: 3.811A 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: 3.548A pdb=" N GLU E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 316 removed outlier: 3.712A pdb=" N ALA E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) removed outlier: 3.871A 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 122 removed outlier: 3.757A pdb=" N ASP A 122 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 214 removed outlier: 5.009A 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 215 through 218 Processing helix chain 'A' and resid 220 through 243 Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.837A pdb=" N ARG A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 4.286A 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 118 through 121 Processing helix chain 'B' and resid 196 through 214 removed outlier: 5.074A 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: 3.714A pdb=" N SER B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 215 through 218' Processing helix chain 'B' and resid 220 through 244 removed outlier: 3.803A pdb=" N THR B 244 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 284 through 315 removed outlier: 3.776A pdb=" N ARG B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 3.982A 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 16 through 20 removed outlier: 6.117A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.507A pdb=" N LYS C 64 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP C 47 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 41 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 38 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N SER C 29 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASN C 40 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N CYS C 27 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N PHE C 42 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE C 25 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N SER C 44 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N TYR C 23 " --> pdb=" O SER C 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 78 removed outlier: 3.598A pdb=" N LEU C 130 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 76 through 78 removed outlier: 3.598A pdb=" N LEU C 130 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 64 through 65 removed outlier: 5.808A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP D 47 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS D 38 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N SER D 29 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASN D 40 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N CYS D 27 " --> pdb=" O ASN D 40 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N PHE D 42 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE D 25 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N SER D 44 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N TYR D 23 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N SER D 46 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N GLY D 21 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N LYS D 48 " --> pdb=" O ASN D 19 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N ASN D 19 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ALA D 143 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL D 18 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 64 through 65 removed outlier: 5.808A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP D 47 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS D 38 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N SER D 29 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASN D 40 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N CYS D 27 " --> pdb=" O ASN D 40 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N PHE D 42 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE D 25 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N SER D 44 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N TYR D 23 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N SER D 46 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N GLY D 21 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N LYS D 48 " --> pdb=" O ASN D 19 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N ASN D 19 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 77 through 78 removed outlier: 10.242A pdb=" N GLU D 181 " --> pdb=" O PRO D 171 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N LYS D 183 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL D 169 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 16 through 20 removed outlier: 6.133A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.239A 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 92 through 94 removed outlier: 3.630A pdb=" N ALA E 41 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR E 36 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU E 30 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE E 42 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU E 24 " --> pdb=" O PHE E 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 77 through 78 removed outlier: 10.958A pdb=" N ARG E 179 " --> pdb=" O ASN E 173 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N ASN E 173 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N GLU E 181 " --> pdb=" O PRO E 171 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N LYS E 183 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL E 169 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.589A pdb=" N VAL A 141 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 18 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 64 through 66 removed outlier: 4.273A pdb=" N ILE A 92 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU A 103 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE A 92 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN A 101 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 104 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR A 36 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU A 30 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N PHE A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU A 24 " --> pdb=" O PHE A 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.960A pdb=" N SER A 164 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N SER A 191 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ILE A 162 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.339A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA B 143 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 22 through 28 removed outlier: 6.486A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 41 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 22 through 28 removed outlier: 6.486A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 41 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 64 " --> pdb=" O VAL B 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.769A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1794 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.45 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: 2141 1.32 - 1.45: 3604 1.45 - 1.57: 7703 1.57 - 1.69: 26 1.69 - 1.81: 35 Bond restraints: 13509 Sorted by residual: bond pdb=" CB TRP D 213 " pdb=" CG TRP D 213 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.06e+00 bond pdb=" C13 PEE B 403 " pdb=" C14 PEE B 403 " ideal model delta sigma weight residual 1.524 1.504 0.020 2.00e-02 2.50e+03 1.05e+00 bond pdb=" N PRO B 7 " pdb=" CA PRO B 7 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.31e-02 5.83e+03 8.50e-01 bond pdb=" CA SER A 182 " pdb=" C SER A 182 " ideal model delta sigma weight residual 1.519 1.529 -0.010 1.14e-02 7.69e+03 7.09e-01 bond pdb=" CB THR A 231 " pdb=" CG2 THR A 231 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.27e-01 ... (remaining 13504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 17820 1.17 - 2.35: 394 2.35 - 3.52: 96 3.52 - 4.70: 7 4.70 - 5.87: 16 Bond angle restraints: 18333 Sorted by residual: angle pdb=" N ILE A 25 " pdb=" CA ILE A 25 " pdb=" C ILE A 25 " ideal model delta sigma weight residual 111.62 109.09 2.53 7.90e-01 1.60e+00 1.03e+01 angle pdb=" C ARG A 118 " pdb=" N TYR A 119 " pdb=" CA TYR A 119 " ideal model delta sigma weight residual 120.97 124.31 -3.34 1.48e+00 4.57e-01 5.09e+00 angle pdb=" C ILE A 202 " pdb=" N LEU A 203 " pdb=" CA LEU A 203 " ideal model delta sigma weight residual 120.09 122.43 -2.34 1.25e+00 6.40e-01 3.49e+00 angle pdb=" N SER A 59 " pdb=" CA SER A 59 " pdb=" C SER A 59 " ideal model delta sigma weight residual 112.54 110.29 2.25 1.22e+00 6.72e-01 3.41e+00 angle pdb=" N ASP E 88 " pdb=" CA ASP E 88 " pdb=" C ASP E 88 " ideal model delta sigma weight residual 107.61 110.80 -3.19 1.74e+00 3.30e-01 3.37e+00 ... (remaining 18328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.56: 7938 32.56 - 65.12: 155 65.12 - 97.68: 23 97.68 - 130.24: 10 130.24 - 162.80: 7 Dihedral angle restraints: 8133 sinusoidal: 3453 harmonic: 4680 Sorted by residual: dihedral pdb=" C4 PEE E 401 " pdb=" O4P PEE E 401 " pdb=" P PEE E 401 " pdb=" O1P PEE E 401 " ideal model delta sinusoidal sigma weight residual 57.28 -139.92 -162.80 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C3 PEE B 404 " pdb=" C1 PEE B 404 " pdb=" C2 PEE B 404 " pdb=" O3P PEE B 404 " ideal model delta sinusoidal sigma weight residual 62.73 -156.75 -140.52 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" O2 PEE B 404 " pdb=" C1 PEE B 404 " pdb=" C2 PEE B 404 " pdb=" O3P PEE B 404 " ideal model delta sinusoidal sigma weight residual -59.96 79.96 -139.92 1 3.00e+01 1.11e-03 1.88e+01 ... (remaining 8130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1241 0.027 - 0.055: 497 0.055 - 0.082: 176 0.082 - 0.109: 143 0.109 - 0.136: 31 Chirality restraints: 2088 Sorted by residual: chirality pdb=" CA ILE E 92 " pdb=" N ILE E 92 " pdb=" C ILE E 92 " pdb=" CB ILE E 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE E 128 " pdb=" N ILE E 128 " pdb=" C ILE E 128 " pdb=" CB ILE E 128 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE B 92 " pdb=" N ILE B 92 " pdb=" C ILE B 92 " pdb=" CB ILE B 92 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 2085 not shown) Planarity restraints: 2251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 67 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.26e+00 pdb=" N PRO C 68 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 68 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 68 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 249 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.95e+00 pdb=" N PRO A 250 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 250 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 250 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 198 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO D 199 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 199 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 199 " 0.018 5.00e-02 4.00e+02 ... (remaining 2248 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 452 2.72 - 3.27: 12311 3.27 - 3.81: 20079 3.81 - 4.36: 24813 4.36 - 4.90: 44137 Nonbonded interactions: 101792 Sorted by model distance: nonbonded pdb=" O LEU A 227 " pdb=" OG1 THR A 231 " model vdw 2.176 3.040 nonbonded pdb=" OH TYR E 28 " pdb=" OE1 GLU A 82 " model vdw 2.195 3.040 nonbonded pdb=" OG SER A 95 " pdb=" OD1 ASP A 97 " model vdw 2.212 3.040 nonbonded pdb=" O PRO B 9 " pdb=" NH2 ARG B 50 " model vdw 2.292 3.120 nonbonded pdb=" O LEU A 209 " pdb=" OG SER A 212 " model vdw 2.304 3.040 ... (remaining 101787 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 316 or (resid 403 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17)))) selection = (chain 'B' and (resid 5 through 316 or (resid 403 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17)))) selection = (chain 'C' and (resid 5 through 316 or (resid 403 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17)))) selection = (chain 'D' and (resid 5 through 316 or (resid 403 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17)))) selection = (chain 'E' and (resid 5 through 316 or (resid 403 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17)))) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.170 Find NCS groups from input model: 0.400 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13509 Z= 0.112 Angle : 0.480 5.869 18333 Z= 0.260 Chirality : 0.041 0.136 2088 Planarity : 0.004 0.045 2251 Dihedral : 14.804 162.796 5083 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.43 % Allowed : 4.93 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.22), residues: 1550 helix: 3.56 (0.21), residues: 491 sheet: -0.06 (0.26), residues: 433 loop : -1.13 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.014 0.001 TYR D 254 PHE 0.009 0.001 PHE D 42 TRP 0.006 0.001 TRP B 160 HIS 0.003 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 (13509) covalent geometry : angle 0.48017 / 0.26 (18333) hydrogen bonds : bond 0.17466 / 12.00 ( 582) hydrogen bonds : angle 6.42655 / 4.47 ( 1794) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 219 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: C 205 MET cc_start: 0.7758 (mmm) cc_final: 0.7554 (mmm) REVERT: D 88 ASP cc_start: 0.8238 (p0) cc_final: 0.7820 (p0) REVERT: E 88 ASP cc_start: 0.8086 (p0) cc_final: 0.7457 (p0) REVERT: E 145 ASP cc_start: 0.8109 (t0) cc_final: 0.7777 (t70) REVERT: A 75 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7002 (mm-30) REVERT: B 5 VAL cc_start: 0.6238 (t) cc_final: 0.5876 (p) REVERT: B 66 TYR cc_start: 0.7651 (m-80) cc_final: 0.7349 (m-80) REVERT: B 76 ILE cc_start: 0.8488 (mt) cc_final: 0.8164 (mm) REVERT: B 109 ARG cc_start: 0.8312 (ptm160) cc_final: 0.7978 (ptm160) REVERT: B 154 ASP cc_start: 0.7454 (t0) cc_final: 0.7139 (t0) REVERT: B 168 VAL cc_start: 0.8044 (m) cc_final: 0.7791 (p) REVERT: B 205 MET cc_start: 0.7986 (mmm) cc_final: 0.7733 (mmt) REVERT: B 243 GLU cc_start: 0.7719 (tp30) cc_final: 0.7351 (tp30) REVERT: B 312 PHE cc_start: 0.7371 (m-10) cc_final: 0.7049 (t80) outliers start: 6 outliers final: 2 residues processed: 224 average time/residue: 0.1222 time to fit residues: 39.0465 Evaluate side-chains 190 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain A residue 135 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.148762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.102519 restraints weight = 15496.206| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.12 r_work: 0.2890 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13509 Z= 0.122 Angle : 0.521 6.185 18333 Z= 0.271 Chirality : 0.043 0.150 2088 Planarity : 0.004 0.047 2251 Dihedral : 15.697 165.841 2160 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.29 % Allowed : 8.43 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.22), residues: 1550 helix: 3.58 (0.21), residues: 490 sheet: 0.08 (0.26), residues: 423 loop : -1.01 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 293 TYR 0.018 0.001 TYR B 251 PHE 0.023 0.001 PHE B 42 TRP 0.013 0.001 TRP B 47 HIS 0.003 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (13509) covalent geometry : angle 0.52079 / 0.27 (18333) hydrogen bonds : bond 0.05779 / 3.84 ( 582) hydrogen bonds : angle 4.60039 / 3.21 ( 1794) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: C 136 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7458 (p0) REVERT: C 205 MET cc_start: 0.7997 (mmm) cc_final: 0.7709 (mmm) REVERT: D 88 ASP cc_start: 0.8274 (p0) cc_final: 0.7863 (p0) REVERT: E 88 ASP cc_start: 0.8405 (p0) cc_final: 0.7740 (p0) REVERT: E 145 ASP cc_start: 0.8138 (t0) cc_final: 0.7800 (t70) REVERT: A 75 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6969 (mm-30) REVERT: B 5 VAL cc_start: 0.6237 (t) cc_final: 0.5928 (p) REVERT: B 66 TYR cc_start: 0.7623 (m-80) cc_final: 0.7341 (m-80) REVERT: B 75 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6903 (tp30) REVERT: B 76 ILE cc_start: 0.8356 (mt) cc_final: 0.8104 (mm) REVERT: B 109 ARG cc_start: 0.8201 (ptm160) cc_final: 0.7942 (ptm160) REVERT: B 154 ASP cc_start: 0.7557 (t0) cc_final: 0.7203 (t0) REVERT: B 168 VAL cc_start: 0.8078 (m) cc_final: 0.7829 (p) REVERT: B 205 MET cc_start: 0.8131 (mmm) cc_final: 0.7826 (mmt) REVERT: B 243 GLU cc_start: 0.7784 (tp30) cc_final: 0.7248 (tp30) REVERT: B 312 PHE cc_start: 0.7452 (m-10) cc_final: 0.7135 (t80) outliers start: 18 outliers final: 8 residues processed: 202 average time/residue: 0.1243 time to fit residues: 35.3503 Evaluate side-chains 183 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 36 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 74 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 chunk 73 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 48 optimal weight: 0.0010 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.148795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.102527 restraints weight = 15581.000| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.12 r_work: 0.2900 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13509 Z= 0.115 Angle : 0.496 6.046 18333 Z= 0.256 Chirality : 0.042 0.140 2088 Planarity : 0.004 0.051 2251 Dihedral : 14.561 175.588 2158 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.79 % Allowed : 8.86 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.22), residues: 1550 helix: 3.67 (0.21), residues: 487 sheet: 0.13 (0.26), residues: 423 loop : -0.96 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 293 TYR 0.017 0.001 TYR B 251 PHE 0.012 0.001 PHE B 42 TRP 0.012 0.001 TRP B 47 HIS 0.003 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (13509) covalent geometry : angle 0.49628 / 0.26 (18333) hydrogen bonds : bond 0.05494 / 3.64 ( 582) hydrogen bonds : angle 4.28934 / 3.01 ( 1794) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: C 51 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.7303 (mtm-85) REVERT: C 136 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7470 (p0) REVERT: C 205 MET cc_start: 0.8012 (mmm) cc_final: 0.7676 (mmm) REVERT: D 88 ASP cc_start: 0.8275 (p0) cc_final: 0.7770 (p0) REVERT: E 75 GLU cc_start: 0.6938 (pm20) cc_final: 0.6468 (pt0) REVERT: E 145 ASP cc_start: 0.8162 (t0) cc_final: 0.7807 (t70) REVERT: E 161 ASP cc_start: 0.8499 (t0) cc_final: 0.8044 (t0) REVERT: A 75 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6897 (mm-30) REVERT: A 133 ARG cc_start: 0.6931 (mtp180) cc_final: 0.6402 (ptp-110) REVERT: B 5 VAL cc_start: 0.6292 (t) cc_final: 0.5944 (p) REVERT: B 66 TYR cc_start: 0.7585 (m-80) cc_final: 0.7381 (m-80) REVERT: B 75 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6745 (tp30) REVERT: B 76 ILE cc_start: 0.8419 (mt) cc_final: 0.8191 (mm) REVERT: B 77 ARG cc_start: 0.8360 (mmm160) cc_final: 0.7376 (mmt90) REVERT: B 91 ASP cc_start: 0.8028 (t0) cc_final: 0.7818 (t0) REVERT: B 109 ARG cc_start: 0.8196 (ptm160) cc_final: 0.7932 (ptm160) REVERT: B 154 ASP cc_start: 0.7584 (t0) cc_final: 0.7361 (t0) REVERT: B 163 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7919 (mp0) REVERT: B 168 VAL cc_start: 0.8050 (m) cc_final: 0.7803 (p) REVERT: B 205 MET cc_start: 0.8035 (mmm) cc_final: 0.7775 (mmt) REVERT: B 243 GLU cc_start: 0.7867 (tp30) cc_final: 0.7262 (tp30) REVERT: B 312 PHE cc_start: 0.7436 (m-10) cc_final: 0.7113 (t80) outliers start: 25 outliers final: 16 residues processed: 208 average time/residue: 0.1105 time to fit residues: 32.5514 Evaluate side-chains 198 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 280 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 0.0270 chunk 140 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 overall best weight: 2.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.144011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.097678 restraints weight = 15774.094| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.10 r_work: 0.2817 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13509 Z= 0.198 Angle : 0.565 6.713 18333 Z= 0.294 Chirality : 0.044 0.140 2088 Planarity : 0.004 0.049 2251 Dihedral : 14.737 177.551 2158 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.21 % Allowed : 10.00 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.22), residues: 1550 helix: 3.41 (0.21), residues: 487 sheet: 0.02 (0.26), residues: 421 loop : -1.10 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 293 TYR 0.015 0.002 TYR D 102 PHE 0.015 0.001 PHE A 106 TRP 0.011 0.001 TRP B 47 HIS 0.003 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 (13509) covalent geometry : angle 0.56537 / 0.29 (18333) hydrogen bonds : bond 0.07584 / 5.07 ( 582) hydrogen bonds : angle 4.52114 / 3.16 ( 1794) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: C 51 ARG cc_start: 0.7594 (mtm-85) cc_final: 0.7342 (mtm-85) REVERT: C 136 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7474 (p0) REVERT: C 205 MET cc_start: 0.8048 (mmm) cc_final: 0.7723 (mmm) REVERT: D 88 ASP cc_start: 0.8355 (p0) cc_final: 0.7927 (p0) REVERT: D 205 MET cc_start: 0.8272 (mmt) cc_final: 0.8060 (mmt) REVERT: E 145 ASP cc_start: 0.8304 (t0) cc_final: 0.7942 (t70) REVERT: A 69 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6581 (tm-30) REVERT: A 75 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6955 (mm-30) REVERT: A 82 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8200 (mt-10) REVERT: A 133 ARG cc_start: 0.6938 (mtp180) cc_final: 0.6512 (ptp-110) REVERT: B 5 VAL cc_start: 0.6262 (t) cc_final: 0.5881 (p) REVERT: B 66 TYR cc_start: 0.7681 (m-80) cc_final: 0.7428 (m-80) REVERT: B 109 ARG cc_start: 0.8276 (ptm160) cc_final: 0.8020 (ptm160) REVERT: B 154 ASP cc_start: 0.7625 (t0) cc_final: 0.7379 (t0) REVERT: B 168 VAL cc_start: 0.8091 (m) cc_final: 0.7852 (p) REVERT: B 205 MET cc_start: 0.8170 (mmt) cc_final: 0.7873 (mmt) REVERT: B 243 GLU cc_start: 0.7921 (tp30) cc_final: 0.7243 (tp30) REVERT: B 280 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8467 (ttmm) outliers start: 31 outliers final: 21 residues processed: 202 average time/residue: 0.1119 time to fit residues: 32.1035 Evaluate side-chains 191 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 280 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 58 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.144961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.099031 restraints weight = 15726.159| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.09 r_work: 0.2866 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13509 Z= 0.178 Angle : 0.545 7.179 18333 Z= 0.283 Chirality : 0.044 0.142 2088 Planarity : 0.004 0.055 2251 Dihedral : 14.491 172.025 2158 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.07 % Allowed : 11.71 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.22), residues: 1550 helix: 3.42 (0.21), residues: 487 sheet: -0.01 (0.26), residues: 423 loop : -1.11 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 293 TYR 0.014 0.001 TYR D 102 PHE 0.012 0.001 PHE A 106 TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (13509) covalent geometry : angle 0.54538 / 0.28 (18333) hydrogen bonds : bond 0.07079 / 4.72 ( 582) hydrogen bonds : angle 4.41656 / 3.07 ( 1794) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: C 51 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.7409 (mtm-85) REVERT: C 136 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7470 (p0) REVERT: C 205 MET cc_start: 0.8014 (mmm) cc_final: 0.7697 (mmm) REVERT: D 205 MET cc_start: 0.8296 (mmt) cc_final: 0.8075 (mmt) REVERT: E 145 ASP cc_start: 0.8388 (t0) cc_final: 0.8009 (t70) REVERT: E 179 ARG cc_start: 0.7022 (mmt90) cc_final: 0.6784 (mmt90) REVERT: A 69 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6667 (tt0) REVERT: A 75 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6997 (mm-30) REVERT: A 133 ARG cc_start: 0.6929 (mtp180) cc_final: 0.6501 (ptp-110) REVERT: A 145 ASP cc_start: 0.7014 (m-30) cc_final: 0.6681 (m-30) REVERT: B 66 TYR cc_start: 0.7651 (m-80) cc_final: 0.7420 (m-80) REVERT: B 154 ASP cc_start: 0.7659 (t0) cc_final: 0.7402 (t0) REVERT: B 168 VAL cc_start: 0.8141 (m) cc_final: 0.7911 (p) REVERT: B 205 MET cc_start: 0.8132 (mmt) cc_final: 0.7818 (mmt) REVERT: B 243 GLU cc_start: 0.7980 (tp30) cc_final: 0.7304 (tp30) outliers start: 29 outliers final: 20 residues processed: 193 average time/residue: 0.1193 time to fit residues: 32.9325 Evaluate side-chains 179 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 180 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 79 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 149 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.149451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.104929 restraints weight = 15563.714| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.22 r_work: 0.2900 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13509 Z= 0.110 Angle : 0.488 7.129 18333 Z= 0.254 Chirality : 0.042 0.143 2088 Planarity : 0.004 0.054 2251 Dihedral : 13.682 168.267 2158 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.36 % Allowed : 12.43 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.22), residues: 1550 helix: 3.61 (0.21), residues: 490 sheet: 0.18 (0.26), residues: 438 loop : -1.06 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 293 TYR 0.014 0.001 TYR D 102 PHE 0.014 0.001 PHE D 195 TRP 0.008 0.001 TRP E 47 HIS 0.003 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (13509) covalent geometry : angle 0.48821 / 0.25 (18333) hydrogen bonds : bond 0.05348 / 3.54 ( 582) hydrogen bonds : angle 4.09015 / 2.85 ( 1794) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: C 51 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.7446 (mtm-85) REVERT: C 136 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7457 (p0) REVERT: C 205 MET cc_start: 0.7955 (mmm) cc_final: 0.7589 (mmm) REVERT: D 205 MET cc_start: 0.8218 (mmt) cc_final: 0.7919 (mmt) REVERT: E 75 GLU cc_start: 0.6881 (pm20) cc_final: 0.6456 (pt0) REVERT: E 88 ASP cc_start: 0.8432 (p0) cc_final: 0.7859 (p0) REVERT: E 145 ASP cc_start: 0.8300 (t0) cc_final: 0.7916 (t70) REVERT: A 69 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6610 (tm-30) REVERT: A 75 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6942 (mm-30) REVERT: A 133 ARG cc_start: 0.6943 (mtp180) cc_final: 0.6529 (ptp-110) REVERT: A 145 ASP cc_start: 0.6960 (m-30) cc_final: 0.6664 (m-30) REVERT: B 154 ASP cc_start: 0.7640 (t0) cc_final: 0.7312 (t0) REVERT: B 168 VAL cc_start: 0.8080 (m) cc_final: 0.7867 (p) REVERT: B 205 MET cc_start: 0.8079 (mmt) cc_final: 0.7782 (mmt) REVERT: B 243 GLU cc_start: 0.7906 (tp30) cc_final: 0.7267 (tp30) REVERT: B 312 PHE cc_start: 0.7511 (m-10) cc_final: 0.7167 (t80) outliers start: 19 outliers final: 14 residues processed: 192 average time/residue: 0.1127 time to fit residues: 31.4378 Evaluate side-chains 184 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 180 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 95 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 173 ASN E 245 ASN A 245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.148482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.103927 restraints weight = 15534.452| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.21 r_work: 0.2882 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13509 Z= 0.129 Angle : 0.501 6.604 18333 Z= 0.260 Chirality : 0.042 0.130 2088 Planarity : 0.004 0.052 2251 Dihedral : 13.486 168.261 2158 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.79 % Allowed : 11.93 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.22), residues: 1550 helix: 3.59 (0.21), residues: 490 sheet: 0.21 (0.26), residues: 437 loop : -1.05 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 293 TYR 0.014 0.001 TYR D 102 PHE 0.010 0.001 PHE B 42 TRP 0.008 0.001 TRP B 47 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (13509) covalent geometry : angle 0.50060 / 0.26 (18333) hydrogen bonds : bond 0.05766 / 3.83 ( 582) hydrogen bonds : angle 4.09763 / 2.85 ( 1794) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: C 51 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7450 (mtm-85) REVERT: C 136 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7420 (p0) REVERT: C 205 MET cc_start: 0.7985 (mmm) cc_final: 0.7600 (mmm) REVERT: D 205 MET cc_start: 0.8231 (mmt) cc_final: 0.7933 (mmt) REVERT: E 75 GLU cc_start: 0.6938 (pm20) cc_final: 0.6495 (pt0) REVERT: E 88 ASP cc_start: 0.8437 (p0) cc_final: 0.7833 (p0) REVERT: E 145 ASP cc_start: 0.8326 (t0) cc_final: 0.7931 (t70) REVERT: A 69 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6608 (tm-30) REVERT: A 75 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6972 (mm-30) REVERT: A 133 ARG cc_start: 0.6920 (mtp180) cc_final: 0.6499 (ptp-110) REVERT: A 145 ASP cc_start: 0.6938 (OUTLIER) cc_final: 0.6637 (m-30) REVERT: B 66 TYR cc_start: 0.7670 (m-80) cc_final: 0.7233 (m-80) REVERT: B 154 ASP cc_start: 0.7622 (t0) cc_final: 0.7283 (t0) REVERT: B 168 VAL cc_start: 0.8081 (m) cc_final: 0.7861 (p) REVERT: B 205 MET cc_start: 0.8127 (mmt) cc_final: 0.7806 (mmt) REVERT: B 243 GLU cc_start: 0.7953 (tp30) cc_final: 0.7266 (tp30) REVERT: B 312 PHE cc_start: 0.7508 (m-10) cc_final: 0.7168 (t80) outliers start: 25 outliers final: 20 residues processed: 189 average time/residue: 0.1183 time to fit residues: 32.1667 Evaluate side-chains 188 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 180 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.147212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101546 restraints weight = 15576.071| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.12 r_work: 0.2859 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13509 Z= 0.127 Angle : 0.498 6.327 18333 Z= 0.259 Chirality : 0.042 0.128 2088 Planarity : 0.004 0.052 2251 Dihedral : 13.171 168.952 2158 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.00 % Allowed : 11.71 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.22), residues: 1550 helix: 3.60 (0.21), residues: 490 sheet: 0.31 (0.26), residues: 431 loop : -1.04 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 293 TYR 0.014 0.001 TYR D 102 PHE 0.014 0.001 PHE D 195 TRP 0.007 0.001 TRP E 47 HIS 0.003 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (13509) covalent geometry : angle 0.49786 / 0.26 (18333) hydrogen bonds : bond 0.05778 / 3.84 ( 582) hydrogen bonds : angle 4.06130 / 2.83 ( 1794) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: C 51 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.7461 (mtm-85) REVERT: C 136 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7451 (p0) REVERT: C 205 MET cc_start: 0.7941 (mmm) cc_final: 0.7553 (mmm) REVERT: D 88 ASP cc_start: 0.8242 (p0) cc_final: 0.7807 (p0) REVERT: D 205 MET cc_start: 0.8236 (mmt) cc_final: 0.7945 (mmt) REVERT: E 75 GLU cc_start: 0.7018 (pm20) cc_final: 0.6561 (pt0) REVERT: E 88 ASP cc_start: 0.8429 (p0) cc_final: 0.7836 (p0) REVERT: E 145 ASP cc_start: 0.8319 (t0) cc_final: 0.7926 (t70) REVERT: A 75 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7046 (mm-30) REVERT: A 133 ARG cc_start: 0.6908 (mtp180) cc_final: 0.6485 (ptp-110) REVERT: A 145 ASP cc_start: 0.6946 (OUTLIER) cc_final: 0.6660 (m-30) REVERT: B 40 ASN cc_start: 0.9292 (m-40) cc_final: 0.9085 (m-40) REVERT: B 66 TYR cc_start: 0.7672 (m-80) cc_final: 0.7284 (m-80) REVERT: B 154 ASP cc_start: 0.7638 (t0) cc_final: 0.7269 (t0) REVERT: B 161 ASP cc_start: 0.7992 (p0) cc_final: 0.7756 (p0) REVERT: B 168 VAL cc_start: 0.8107 (m) cc_final: 0.7885 (p) REVERT: B 205 MET cc_start: 0.8129 (mmt) cc_final: 0.7808 (mmt) REVERT: B 243 GLU cc_start: 0.7934 (tp30) cc_final: 0.7261 (tp30) REVERT: B 312 PHE cc_start: 0.7517 (m-10) cc_final: 0.7156 (t80) outliers start: 28 outliers final: 21 residues processed: 193 average time/residue: 0.1082 time to fit residues: 30.3334 Evaluate side-chains 191 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 180 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 100 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.147735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.102484 restraints weight = 15608.229| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.13 r_work: 0.2841 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13509 Z= 0.150 Angle : 0.517 6.496 18333 Z= 0.269 Chirality : 0.043 0.132 2088 Planarity : 0.004 0.051 2251 Dihedral : 13.196 172.500 2158 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.21 % Allowed : 11.43 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.22), residues: 1550 helix: 3.58 (0.21), residues: 487 sheet: 0.31 (0.26), residues: 431 loop : -1.05 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 293 TYR 0.014 0.001 TYR D 102 PHE 0.010 0.001 PHE A 106 TRP 0.006 0.001 TRP E 47 HIS 0.003 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (13509) covalent geometry : angle 0.51712 / 0.27 (18333) hydrogen bonds : bond 0.06336 / 4.22 ( 582) hydrogen bonds : angle 4.13795 / 2.88 ( 1794) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.324 Fit side-chains REVERT: C 51 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7480 (mtm-85) REVERT: C 136 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7481 (p0) REVERT: C 205 MET cc_start: 0.7980 (mmm) cc_final: 0.7606 (mmm) REVERT: D 88 ASP cc_start: 0.8251 (p0) cc_final: 0.7815 (p0) REVERT: D 205 MET cc_start: 0.8275 (mmt) cc_final: 0.7998 (mmt) REVERT: E 75 GLU cc_start: 0.7005 (pm20) cc_final: 0.6578 (pt0) REVERT: E 88 ASP cc_start: 0.8459 (p0) cc_final: 0.7828 (p0) REVERT: E 145 ASP cc_start: 0.8348 (t0) cc_final: 0.7983 (t70) REVERT: A 45 LEU cc_start: 0.7793 (mt) cc_final: 0.7184 (tt) REVERT: A 75 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7107 (mm-30) REVERT: A 82 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8160 (mt-10) REVERT: A 133 ARG cc_start: 0.6942 (mtp180) cc_final: 0.6518 (ptp-110) REVERT: A 145 ASP cc_start: 0.6899 (OUTLIER) cc_final: 0.6618 (m-30) REVERT: B 66 TYR cc_start: 0.7670 (m-80) cc_final: 0.7330 (m-80) REVERT: B 154 ASP cc_start: 0.7670 (t0) cc_final: 0.7302 (t0) REVERT: B 161 ASP cc_start: 0.8042 (p0) cc_final: 0.7792 (p0) REVERT: B 168 VAL cc_start: 0.8107 (m) cc_final: 0.7890 (p) REVERT: B 205 MET cc_start: 0.8154 (mmt) cc_final: 0.7827 (mmt) REVERT: B 243 GLU cc_start: 0.7918 (tp30) cc_final: 0.7248 (tp30) outliers start: 31 outliers final: 26 residues processed: 195 average time/residue: 0.1026 time to fit residues: 28.7796 Evaluate side-chains 195 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 66 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.147708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.102413 restraints weight = 15504.562| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.11 r_work: 0.2862 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13509 Z= 0.129 Angle : 0.503 6.597 18333 Z= 0.262 Chirality : 0.042 0.128 2088 Planarity : 0.004 0.051 2251 Dihedral : 12.962 175.142 2158 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.00 % Allowed : 11.57 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.22), residues: 1550 helix: 3.61 (0.21), residues: 487 sheet: 0.34 (0.26), residues: 431 loop : -1.02 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 293 TYR 0.014 0.001 TYR D 102 PHE 0.014 0.001 PHE D 195 TRP 0.008 0.001 TRP E 47 HIS 0.003 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (13509) covalent geometry : angle 0.50280 / 0.26 (18333) hydrogen bonds : bond 0.05886 / 3.91 ( 582) hydrogen bonds : angle 4.05929 / 2.82 ( 1794) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3100 Ramachandran restraints generated. 1550 Oldfield, 0 Emsley, 1550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: C 51 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7487 (mtm-85) REVERT: C 136 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7488 (p0) REVERT: C 205 MET cc_start: 0.7959 (mmm) cc_final: 0.7594 (mmm) REVERT: D 88 ASP cc_start: 0.8267 (p0) cc_final: 0.7832 (p0) REVERT: D 205 MET cc_start: 0.8261 (mmt) cc_final: 0.7975 (mmt) REVERT: E 75 GLU cc_start: 0.7009 (pm20) cc_final: 0.6581 (pt0) REVERT: E 145 ASP cc_start: 0.8335 (t0) cc_final: 0.7971 (t70) REVERT: A 75 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7081 (mm-30) REVERT: A 82 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8158 (mt-10) REVERT: A 133 ARG cc_start: 0.6898 (mtp180) cc_final: 0.6488 (ptp-110) REVERT: A 145 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.6596 (m-30) REVERT: B 66 TYR cc_start: 0.7665 (m-80) cc_final: 0.7331 (m-80) REVERT: B 154 ASP cc_start: 0.7642 (t0) cc_final: 0.7275 (t0) REVERT: B 161 ASP cc_start: 0.8028 (p0) cc_final: 0.7796 (p0) REVERT: B 168 VAL cc_start: 0.8118 (m) cc_final: 0.7909 (p) REVERT: B 205 MET cc_start: 0.8141 (mmt) cc_final: 0.7835 (mmt) REVERT: B 243 GLU cc_start: 0.7894 (tp30) cc_final: 0.7232 (tp30) REVERT: B 312 PHE cc_start: 0.7519 (m-10) cc_final: 0.7179 (t80) outliers start: 28 outliers final: 25 residues processed: 190 average time/residue: 0.1061 time to fit residues: 28.9900 Evaluate side-chains 192 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 138 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 115 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.149033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.103848 restraints weight = 15487.018| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.13 r_work: 0.2868 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13509 Z= 0.127 Angle : 0.505 6.582 18333 Z= 0.264 Chirality : 0.043 0.141 2088 Planarity : 0.004 0.050 2251 Dihedral : 12.848 177.796 2158 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.07 % Allowed : 11.71 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.22), residues: 1550 helix: 3.62 (0.21), residues: 487 sheet: 0.34 (0.26), residues: 431 loop : -1.01 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 293 TYR 0.014 0.001 TYR D 102 PHE 0.010 0.001 PHE B 42 TRP 0.007 0.001 TRP E 47 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (13509) covalent geometry : angle 0.50493 / 0.26 (18333) hydrogen bonds : bond 0.05795 / 3.85 ( 582) hydrogen bonds : angle 4.03828 / 2.81 ( 1794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3155.77 seconds wall clock time: 54 minutes 35.68 seconds (3275.68 seconds total)