Starting phenix.real_space_refine on Wed Feb 4 22:56:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lai_62929/02_2026/9lai_62929.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lai_62929/02_2026/9lai_62929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lai_62929/02_2026/9lai_62929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lai_62929/02_2026/9lai_62929.map" model { file = "/net/cci-nas-00/data/ceres_data/9lai_62929/02_2026/9lai_62929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lai_62929/02_2026/9lai_62929.cif" } resolution = 3.08 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 20 5.49 5 S 20 5.16 5 Cl 5 4.86 5 C 8890 2.51 5 N 2034 2.21 5 O 2431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13400 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain: "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: "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: "D" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 147 Unusual residues: {' CL': 1, 'PEE': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 177 Unusual residues: {' CL': 1, 'PEE': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' CL': 1, 'PEE': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 193 Unusual residues: {' CL': 1, 'PEE': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {' CL': 1, 'PEE': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 44 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG D 293 " occ=0.51 ... (20 atoms not shown) pdb=" NH2BARG D 293 " occ=0.49 Time building chain proxies: 4.20, per 1000 atoms: 0.31 Number of scatterers: 13400 At special positions: 0 Unit cell: (101.84, 95, 128.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 5 17.00 S 20 16.00 P 20 15.00 O 2431 8.00 N 2034 7.00 C 8890 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 695.1 milliseconds 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3052 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 17 sheets defined 38.2% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 196 through 213 removed outlier: 4.849A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.636A pdb=" N SER A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 244 removed outlier: 3.955A pdb=" N THR A 244 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.628A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 67 through 71 removed outlier: 4.266A pdb=" N ILE B 71 " --> pdb=" O PRO B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 196 through 214 removed outlier: 5.046A 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: 3.683A pdb=" N SER B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 215 through 218' Processing helix chain 'B' and resid 220 through 244 removed outlier: 4.114A 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: 3.832A pdb=" N ARG B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'C' and resid 57 through 61 removed outlier: 4.001A pdb=" N VAL C 61 " --> pdb=" O ARG C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 removed outlier: 4.169A pdb=" N ILE C 71 " --> pdb=" O PRO C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 196 through 214 removed outlier: 5.028A 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 215 through 218 removed outlier: 3.749A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 218' Processing helix chain 'C' and resid 220 through 244 removed outlier: 4.005A pdb=" N THR C 244 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 284 through 315 removed outlier: 3.774A pdb=" N ARG C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 146 through 149 removed outlier: 3.796A 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: 3.532A pdb=" N ASN E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 214 removed outlier: 3.709A pdb=" N MET E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 206 " --> pdb=" O ILE E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 218 removed outlier: 3.704A 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 243 Processing helix chain 'E' and resid 253 through 282 Processing helix chain 'E' and resid 284 through 316 removed outlier: 3.565A pdb=" N ALA E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 196 through 213 removed outlier: 5.379A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Proline residue: D 204 - end of helix Processing helix chain 'D' and resid 214 through 218 removed outlier: 3.664A pdb=" N SER D 218 " --> pdb=" O ALA D 215 " (cutoff:3.500A) 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 315 removed outlier: 3.576A pdb=" N ALA D 288 " --> pdb=" O GLN D 284 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE D 297 " --> pdb=" O AARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 111 removed outlier: 5.841A pdb=" N PHE A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU A 24 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER A 44 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE A 22 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER A 46 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR A 20 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 111 removed outlier: 5.841A pdb=" N PHE A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU A 24 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER A 44 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE A 22 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER A 46 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR A 20 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLY A 150 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A 22 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.514A pdb=" N LEU A 130 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 28 removed outlier: 5.737A pdb=" N LEU B 24 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N PHE B 42 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 43 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU B 45 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR B 102 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN B 101 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE B 92 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 103 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 94 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 24 through 28 removed outlier: 5.737A pdb=" N LEU B 24 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N PHE B 42 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA B 143 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 5.540A pdb=" N VAL B 132 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER B 182 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER B 164 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N SER B 191 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE B 162 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 44 through 47 removed outlier: 6.699A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 64 through 65 removed outlier: 4.833A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR C 36 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU C 30 " --> pdb=" O THR C 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 78 removed outlier: 3.510A pdb=" N ILE C 190 " --> pdb=" O GLN C 124 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL C 132 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER C 182 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS C 183 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL C 169 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 64 through 65 removed outlier: 5.839A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP E 47 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 45 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N THR E 36 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER E 29 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 64 through 65 removed outlier: 5.839A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP E 47 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 45 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N THR E 36 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER E 29 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 77 through 78 removed outlier: 3.566A pdb=" N SER E 182 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASP E 185 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER E 164 " --> pdb=" O ARG E 189 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER E 191 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE E 162 " --> pdb=" O SER E 191 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 77 through 78 removed outlier: 3.566A pdb=" N SER E 182 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 16 through 17 removed outlier: 6.164A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 92 through 94 removed outlier: 3.584A pdb=" N LEU D 43 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR D 36 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER D 29 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N CYS D 27 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN D 40 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR D 23 " --> pdb=" O PHE D 42 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 76 through 78 removed outlier: 7.262A pdb=" N LYS D 183 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL D 169 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1804 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: 2.18 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2124 1.32 - 1.44: 3678 1.44 - 1.56: 7835 1.56 - 1.69: 40 1.69 - 1.81: 35 Bond restraints: 13712 Sorted by residual: bond pdb=" CB TRP E 213 " pdb=" CG TRP E 213 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.48e+00 bond pdb=" C13 PEE B 405 " pdb=" C14 PEE B 405 " ideal model delta sigma weight residual 1.524 1.503 0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" C13 PEE C 405 " pdb=" C14 PEE C 405 " ideal model delta sigma weight residual 1.524 1.503 0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" C13 PEE A 404 " pdb=" C14 PEE A 404 " ideal model delta sigma weight residual 1.524 1.503 0.021 2.00e-02 2.50e+03 1.06e+00 bond pdb=" CA PRO E 7 " pdb=" C PRO E 7 " ideal model delta sigma weight residual 1.514 1.509 0.005 5.50e-03 3.31e+04 9.57e-01 ... (remaining 13707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 17999 1.21 - 2.42: 448 2.42 - 3.63: 101 3.63 - 4.83: 21 4.83 - 6.04: 9 Bond angle restraints: 18578 Sorted by residual: angle pdb=" N ILE D 25 " pdb=" CA ILE D 25 " pdb=" C ILE D 25 " ideal model delta sigma weight residual 111.67 108.75 2.92 9.50e-01 1.11e+00 9.46e+00 angle pdb=" N ASP A 153 " pdb=" CA ASP A 153 " pdb=" C ASP A 153 " ideal model delta sigma weight residual 113.38 110.70 2.68 1.17e+00 7.31e-01 5.25e+00 angle pdb=" N ILE C 201 " pdb=" CA ILE C 201 " pdb=" C ILE C 201 " ideal model delta sigma weight residual 109.34 113.34 -4.00 2.08e+00 2.31e-01 3.70e+00 angle pdb=" N ILE B 201 " pdb=" CA ILE B 201 " pdb=" C ILE B 201 " ideal model delta sigma weight residual 109.34 113.34 -4.00 2.08e+00 2.31e-01 3.70e+00 angle pdb=" N GLU E 243 " pdb=" CA GLU E 243 " pdb=" C GLU E 243 " ideal model delta sigma weight residual 112.34 114.82 -2.48 1.30e+00 5.92e-01 3.63e+00 ... (remaining 18573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 8050 35.36 - 70.72: 201 70.72 - 106.09: 22 106.09 - 141.45: 17 141.45 - 176.81: 11 Dihedral angle restraints: 8301 sinusoidal: 3617 harmonic: 4684 Sorted by residual: dihedral pdb=" O2 PEE E 407 " pdb=" C1 PEE E 407 " pdb=" C2 PEE E 407 " pdb=" O3P PEE E 407 " ideal model delta sinusoidal sigma weight residual 300.04 123.23 176.81 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PEE E 407 " pdb=" C1 PEE E 407 " pdb=" C2 PEE E 407 " pdb=" O3P PEE E 407 " ideal model delta sinusoidal sigma weight residual 62.73 -111.72 174.45 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C4 PEE B 406 " pdb=" O4P PEE B 406 " pdb=" P PEE B 406 " pdb=" O3P PEE B 406 " ideal model delta sinusoidal sigma weight residual 171.78 -27.65 -160.57 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 8298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1199 0.027 - 0.054: 516 0.054 - 0.080: 195 0.080 - 0.107: 139 0.107 - 0.134: 47 Chirality restraints: 2096 Sorted by residual: chirality pdb=" CA ILE D 71 " pdb=" N ILE D 71 " pdb=" C ILE D 71 " pdb=" CB ILE D 71 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE E 73 " pdb=" N ILE E 73 " pdb=" C ILE E 73 " pdb=" CB ILE E 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA PHE C 299 " pdb=" N PHE C 299 " pdb=" C PHE C 299 " pdb=" CB PHE C 299 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 2093 not shown) Planarity restraints: 2268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 67 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO B 68 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 68 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 68 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 249 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO D 250 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 250 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 250 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 249 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 250 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 250 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 250 " -0.018 5.00e-02 4.00e+02 ... (remaining 2265 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2369 2.77 - 3.31: 12092 3.31 - 3.84: 20444 3.84 - 4.37: 24137 4.37 - 4.90: 43504 Nonbonded interactions: 102546 Sorted by model distance: nonbonded pdb=" O LEU A 227 " pdb=" OG1 THR A 231 " model vdw 2.242 3.040 nonbonded pdb=" O ILE C 76 " pdb=" NH1 ARG C 85 " model vdw 2.280 3.120 nonbonded pdb=" O LEU C 227 " pdb=" OG1 THR C 231 " model vdw 2.310 3.040 nonbonded pdb=" OE1 GLU B 163 " pdb=" NH1 ARG B 189 " model vdw 2.337 3.120 nonbonded pdb=" OH TYR D 102 " pdb=" OE2 GLU D 104 " model vdw 2.338 3.040 ... (remaining 102541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name O1P or name O2 or name O2P or name O3 or name O3P or name \ O4 or name O4P or name O5 or name P )) or (resid 404 and (name C13 or name C14 o \ r name C15 or name C16 or name C17 or name C18 or name C19)))) selection = (chain 'B' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name O1P or name O2 or name O2P or name O3 or name O3P or name \ O4 or name O4P or name O5 or name P )) or (resid 404 and (name C13 or name C14 o \ r name C15 or name C16 or name C17 or name C18 or name C19)))) selection = (chain 'C' and (resid 5 through 292 or resid 294 through 316 or resid 403 or (re \ sid 404 and (name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19)))) selection = (chain 'D' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name O1P or name O2 or name O2P or name O3 or name O3P or name \ O4 or name O4P or name O5 or name P )) or (resid 404 and (name C13 or name C14 o \ r name C15 or name C16 or name C17 or name C18 or name C19)))) selection = (chain 'E' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C20 or name C21 or name C22 or name C23 or name \ C24 or name C3 or name O1P or name O2 or name O2P or name O3 or name O3P or nam \ e O4 or name O4P or name O5 or name P )) or (resid 404 and (name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.420 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13712 Z= 0.135 Angle : 0.516 6.043 18578 Z= 0.270 Chirality : 0.042 0.134 2096 Planarity : 0.004 0.042 2268 Dihedral : 17.811 176.809 5249 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.21 % Allowed : 6.50 % Favored : 92.29 % 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: 0.30 (0.22), residues: 1553 helix: 2.98 (0.21), residues: 518 sheet: -1.07 (0.27), residues: 360 loop : -1.34 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.013 0.001 TYR D 254 PHE 0.011 0.001 PHE B 156 TRP 0.006 0.001 TRP A 160 HIS 0.002 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00304 (13712) covalent geometry : angle 0.51606 (18578) hydrogen bonds : bond 0.17014 ( 579) hydrogen bonds : angle 6.64171 ( 1804) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.500 Fit side-chains REVERT: A 280 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8420 (ttpp) REVERT: C 88 ASP cc_start: 0.7739 (t70) cc_final: 0.7416 (t0) REVERT: C 102 TYR cc_start: 0.6944 (t80) cc_final: 0.6638 (t80) REVERT: C 109 ARG cc_start: 0.8167 (ttm110) cc_final: 0.7952 (ttm110) REVERT: C 161 ASP cc_start: 0.7657 (p0) cc_final: 0.7400 (p0) REVERT: E 176 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7502 (tt) REVERT: E 252 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8499 (tpt) outliers start: 17 outliers final: 7 residues processed: 205 average time/residue: 0.1178 time to fit residues: 35.6950 Evaluate side-chains 177 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain D residue 212 SER 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: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 245 ASN B 187 GLN C 19 ASN D 245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.167613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.099786 restraints weight = 26694.120| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.01 r_work: 0.2834 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 13712 Z= 0.270 Angle : 0.658 8.121 18578 Z= 0.341 Chirality : 0.047 0.153 2096 Planarity : 0.005 0.046 2268 Dihedral : 20.719 174.853 2334 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.28 % Allowed : 9.21 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.22), residues: 1553 helix: 2.71 (0.21), residues: 519 sheet: -0.90 (0.27), residues: 356 loop : -1.48 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 189 TYR 0.021 0.002 TYR E 102 PHE 0.014 0.002 PHE C 37 TRP 0.010 0.002 TRP A 47 HIS 0.003 0.001 HIS E 235 Details of bonding type rmsd covalent geometry : bond 0.00680 (13712) covalent geometry : angle 0.65759 (18578) hydrogen bonds : bond 0.08925 ( 579) hydrogen bonds : angle 5.09815 ( 1804) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.509 Fit side-chains REVERT: A 26 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6558 (mm-30) REVERT: A 122 ASP cc_start: 0.8749 (p0) cc_final: 0.8518 (p0) REVERT: C 88 ASP cc_start: 0.7827 (t70) cc_final: 0.7572 (t0) REVERT: C 102 TYR cc_start: 0.6960 (t80) cc_final: 0.6751 (t80) outliers start: 32 outliers final: 25 residues processed: 194 average time/residue: 0.1213 time to fit residues: 34.8987 Evaluate side-chains 193 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 244 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 140 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 245 ASN B 40 ASN B 187 GLN C 19 ASN D 40 ASN D 245 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.171123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.104772 restraints weight = 19472.005| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.68 r_work: 0.2928 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13712 Z= 0.131 Angle : 0.539 8.028 18578 Z= 0.279 Chirality : 0.043 0.162 2096 Planarity : 0.004 0.044 2268 Dihedral : 19.642 171.479 2327 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.00 % Allowed : 11.35 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1553 helix: 3.08 (0.21), residues: 519 sheet: -0.58 (0.26), residues: 382 loop : -1.44 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.013 0.001 TYR E 102 PHE 0.018 0.001 PHE C 106 TRP 0.007 0.001 TRP A 160 HIS 0.002 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00299 (13712) covalent geometry : angle 0.53901 (18578) hydrogen bonds : bond 0.06586 ( 579) hydrogen bonds : angle 4.56033 ( 1804) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.497 Fit side-chains REVERT: C 88 ASP cc_start: 0.7869 (t70) cc_final: 0.7652 (t0) REVERT: C 133 ARG cc_start: 0.6569 (ptm160) cc_final: 0.6205 (ptm160) outliers start: 28 outliers final: 19 residues processed: 201 average time/residue: 0.1098 time to fit residues: 33.3880 Evaluate side-chains 190 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 58 optimal weight: 0.4980 chunk 59 optimal weight: 0.4980 chunk 8 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 129 optimal weight: 0.0870 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN B 187 GLN C 19 ASN E 173 ASN D 200 ASN D 245 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.172588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.105438 restraints weight = 25234.381| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.00 r_work: 0.2958 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13712 Z= 0.123 Angle : 0.531 8.383 18578 Z= 0.273 Chirality : 0.043 0.155 2096 Planarity : 0.004 0.042 2268 Dihedral : 19.077 169.804 2327 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.21 % Allowed : 11.99 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.22), residues: 1553 helix: 3.18 (0.21), residues: 519 sheet: -0.44 (0.27), residues: 389 loop : -1.35 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 189 TYR 0.025 0.001 TYR D 102 PHE 0.012 0.001 PHE C 37 TRP 0.007 0.001 TRP A 160 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00275 (13712) covalent geometry : angle 0.53121 (18578) hydrogen bonds : bond 0.06024 ( 579) hydrogen bonds : angle 4.35680 ( 1804) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.525 Fit side-chains REVERT: A 26 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6368 (mm-30) REVERT: A 122 ASP cc_start: 0.8713 (p0) cc_final: 0.8480 (p0) REVERT: B 161 ASP cc_start: 0.8122 (p0) cc_final: 0.7862 (p0) REVERT: C 133 ARG cc_start: 0.6539 (ptm160) cc_final: 0.6290 (ptm160) REVERT: C 312 PHE cc_start: 0.7597 (m-10) cc_final: 0.7215 (t80) REVERT: E 176 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8257 (tt) REVERT: D 77 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7758 (mtt-85) outliers start: 31 outliers final: 22 residues processed: 197 average time/residue: 0.1105 time to fit residues: 32.9886 Evaluate side-chains 199 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 244 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 111 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN B 187 GLN E 173 ASN D 200 ASN D 245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.170217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.104113 restraints weight = 21208.978| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.75 r_work: 0.2885 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13712 Z= 0.174 Angle : 0.560 7.187 18578 Z= 0.289 Chirality : 0.044 0.154 2096 Planarity : 0.004 0.045 2268 Dihedral : 18.738 170.539 2327 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.86 % Allowed : 12.78 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.22), residues: 1553 helix: 3.03 (0.21), residues: 519 sheet: -0.45 (0.27), residues: 382 loop : -1.39 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 189 TYR 0.021 0.001 TYR D 102 PHE 0.013 0.001 PHE C 37 TRP 0.008 0.001 TRP A 160 HIS 0.002 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00428 (13712) covalent geometry : angle 0.55951 (18578) hydrogen bonds : bond 0.07189 ( 579) hydrogen bonds : angle 4.40768 ( 1804) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.497 Fit side-chains REVERT: A 26 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6248 (mm-30) REVERT: A 33 LYS cc_start: 0.5360 (OUTLIER) cc_final: 0.4985 (mtmm) REVERT: B 161 ASP cc_start: 0.8107 (p0) cc_final: 0.7839 (p0) REVERT: C 133 ARG cc_start: 0.6549 (ptm160) cc_final: 0.6262 (ptm160) outliers start: 40 outliers final: 28 residues processed: 201 average time/residue: 0.1061 time to fit residues: 32.0732 Evaluate side-chains 204 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 244 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 119 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN B 187 GLN E 173 ASN D 40 ASN D 200 ASN D 245 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.170912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.104301 restraints weight = 21117.134| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.78 r_work: 0.2840 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13712 Z= 0.156 Angle : 0.551 8.069 18578 Z= 0.283 Chirality : 0.043 0.155 2096 Planarity : 0.004 0.044 2268 Dihedral : 18.332 172.034 2326 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.86 % Allowed : 13.13 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.22), residues: 1553 helix: 3.09 (0.21), residues: 519 sheet: -0.40 (0.27), residues: 382 loop : -1.38 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.024 0.001 TYR C 102 PHE 0.021 0.001 PHE C 106 TRP 0.008 0.001 TRP A 160 HIS 0.002 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00379 (13712) covalent geometry : angle 0.55073 (18578) hydrogen bonds : bond 0.06805 ( 579) hydrogen bonds : angle 4.31524 ( 1804) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.519 Fit side-chains REVERT: A 26 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6275 (mm-30) REVERT: A 33 LYS cc_start: 0.5287 (OUTLIER) cc_final: 0.4911 (mtmm) REVERT: A 122 ASP cc_start: 0.8589 (p0) cc_final: 0.8336 (p0) REVERT: B 161 ASP cc_start: 0.8021 (p0) cc_final: 0.7784 (p0) REVERT: C 109 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7790 (ttm110) REVERT: C 133 ARG cc_start: 0.6568 (ptm160) cc_final: 0.6255 (ptm160) outliers start: 40 outliers final: 29 residues processed: 207 average time/residue: 0.1125 time to fit residues: 34.8087 Evaluate side-chains 209 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 244 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 57 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 82 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN B 187 GLN E 173 ASN D 40 ASN D 200 ASN D 245 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.171711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115536 restraints weight = 28223.091| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 5.01 r_work: 0.2805 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 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 0.035 13712 Z= 0.136 Angle : 0.545 9.717 18578 Z= 0.279 Chirality : 0.043 0.213 2096 Planarity : 0.004 0.042 2268 Dihedral : 17.991 172.506 2326 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.57 % Allowed : 13.99 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.22), residues: 1553 helix: 3.16 (0.21), residues: 519 sheet: -0.35 (0.27), residues: 389 loop : -1.31 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 109 TYR 0.028 0.001 TYR C 102 PHE 0.021 0.001 PHE C 106 TRP 0.008 0.001 TRP A 160 HIS 0.002 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00318 (13712) covalent geometry : angle 0.54519 (18578) hydrogen bonds : bond 0.06355 ( 579) hydrogen bonds : angle 4.24371 ( 1804) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.486 Fit side-chains REVERT: A 26 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6398 (mm-30) REVERT: A 33 LYS cc_start: 0.5320 (OUTLIER) cc_final: 0.4935 (mtmm) REVERT: A 122 ASP cc_start: 0.8724 (p0) cc_final: 0.8522 (p0) REVERT: B 161 ASP cc_start: 0.8107 (p0) cc_final: 0.7880 (p0) REVERT: C 44 SER cc_start: 0.7364 (t) cc_final: 0.6664 (p) REVERT: C 102 TYR cc_start: 0.6976 (t80) cc_final: 0.6659 (t80) REVERT: C 109 ARG cc_start: 0.8232 (ttm110) cc_final: 0.8000 (ttm110) REVERT: C 133 ARG cc_start: 0.6545 (ptm160) cc_final: 0.6239 (ptm160) outliers start: 36 outliers final: 29 residues processed: 203 average time/residue: 0.1117 time to fit residues: 33.8083 Evaluate side-chains 211 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 244 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 136 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN B 187 GLN C 19 ASN E 173 ASN D 245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.164382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.098463 restraints weight = 23113.509| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.82 r_work: 0.2795 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.072 13712 Z= 0.399 Angle : 0.751 8.494 18578 Z= 0.385 Chirality : 0.051 0.204 2096 Planarity : 0.005 0.057 2268 Dihedral : 18.982 177.649 2326 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.35 % Allowed : 13.35 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.22), residues: 1553 helix: 2.50 (0.21), residues: 519 sheet: -0.60 (0.27), residues: 378 loop : -1.68 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 118 TYR 0.024 0.003 TYR C 102 PHE 0.019 0.002 PHE C 195 TRP 0.017 0.003 TRP B 213 HIS 0.004 0.001 HIS E 235 Details of bonding type rmsd covalent geometry : bond 0.01010 (13712) covalent geometry : angle 0.75103 (18578) hydrogen bonds : bond 0.10451 ( 579) hydrogen bonds : angle 4.81902 ( 1804) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 0.425 Fit side-chains REVERT: A 26 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6219 (mm-30) REVERT: C 82 GLU cc_start: 0.8790 (tp30) cc_final: 0.8585 (tp30) REVERT: C 133 ARG cc_start: 0.6699 (ptm160) cc_final: 0.6341 (ptm160) outliers start: 47 outliers final: 38 residues processed: 192 average time/residue: 0.1142 time to fit residues: 33.1537 Evaluate side-chains 202 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 244 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 48 optimal weight: 10.0000 chunk 6 optimal weight: 0.0070 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 86 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN B 187 GLN B 245 ASN C 19 ASN E 173 ASN D 40 ASN D 200 ASN D 245 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.171969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.104941 restraints weight = 25722.695| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.01 r_work: 0.2865 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13712 Z= 0.121 Angle : 0.545 9.333 18578 Z= 0.281 Chirality : 0.043 0.158 2096 Planarity : 0.004 0.047 2268 Dihedral : 17.965 176.633 2326 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.21 % Allowed : 14.92 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.22), residues: 1553 helix: 3.14 (0.21), residues: 519 sheet: -0.39 (0.27), residues: 387 loop : -1.39 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 118 TYR 0.031 0.001 TYR C 102 PHE 0.023 0.001 PHE C 106 TRP 0.009 0.001 TRP E 213 HIS 0.002 0.001 HIS D 277 Details of bonding type rmsd covalent geometry : bond 0.00258 (13712) covalent geometry : angle 0.54479 (18578) hydrogen bonds : bond 0.05936 ( 579) hydrogen bonds : angle 4.27032 ( 1804) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.533 Fit side-chains REVERT: A 26 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6328 (mm-30) REVERT: A 122 ASP cc_start: 0.8642 (p0) cc_final: 0.8396 (p0) REVERT: B 231 THR cc_start: 0.9468 (m) cc_final: 0.9217 (m) REVERT: C 44 SER cc_start: 0.7205 (t) cc_final: 0.6496 (p) REVERT: C 82 GLU cc_start: 0.8841 (tp30) cc_final: 0.8610 (tp30) REVERT: C 109 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7826 (ttm110) REVERT: C 133 ARG cc_start: 0.6493 (ptm160) cc_final: 0.6179 (ptm160) outliers start: 31 outliers final: 27 residues processed: 202 average time/residue: 0.1121 time to fit residues: 34.0865 Evaluate side-chains 201 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.0040 chunk 54 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 141 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN C 19 ASN E 173 ASN D 200 ASN D 245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.172007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114272 restraints weight = 18757.045| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.78 r_work: 0.2954 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 13712 Z= 0.171 Angle : 0.859 59.200 18578 Z= 0.508 Chirality : 0.046 0.625 2096 Planarity : 0.005 0.132 2268 Dihedral : 17.965 176.638 2326 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.68 % Rotamer: Outliers : 2.07 % Allowed : 15.06 % Favored : 82.87 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.22), residues: 1553 helix: 3.15 (0.21), residues: 519 sheet: -0.37 (0.27), residues: 387 loop : -1.39 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 85 TYR 0.019 0.001 TYR D 102 PHE 0.021 0.001 PHE C 106 TRP 0.009 0.001 TRP E 213 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00339 (13712) covalent geometry : angle 0.85852 (18578) hydrogen bonds : bond 0.06036 ( 579) hydrogen bonds : angle 4.25851 ( 1804) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.605 Fit side-chains REVERT: A 26 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6352 (mm-30) REVERT: A 245 ASN cc_start: 0.8218 (p0) cc_final: 0.7796 (p0) REVERT: B 231 THR cc_start: 0.9488 (m) cc_final: 0.9231 (m) REVERT: C 44 SER cc_start: 0.7244 (t) cc_final: 0.6539 (p) REVERT: C 82 GLU cc_start: 0.8819 (tp30) cc_final: 0.8593 (tp30) REVERT: C 109 ARG cc_start: 0.8116 (ttm110) cc_final: 0.7851 (ttm110) REVERT: C 133 ARG cc_start: 0.6488 (ptm160) cc_final: 0.6178 (ptm160) outliers start: 29 outliers final: 27 residues processed: 194 average time/residue: 0.1154 time to fit residues: 33.6321 Evaluate side-chains 199 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 21 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN C 19 ASN E 173 ASN D 40 ASN D 200 ASN D 245 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.172035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103996 restraints weight = 30172.484| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.27 r_work: 0.2882 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 13712 Z= 0.171 Angle : 0.859 59.200 18578 Z= 0.508 Chirality : 0.046 0.625 2096 Planarity : 0.005 0.132 2268 Dihedral : 17.965 176.638 2326 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.68 % Rotamer: Outliers : 2.00 % Allowed : 15.06 % Favored : 82.94 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.22), residues: 1553 helix: 3.15 (0.21), residues: 519 sheet: -0.37 (0.27), residues: 387 loop : -1.39 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 85 TYR 0.019 0.001 TYR D 102 PHE 0.021 0.001 PHE C 106 TRP 0.009 0.001 TRP E 213 HIS 0.002 0.001 HIS C 277 Details of bonding type rmsd covalent geometry : bond 0.00339 (13712) covalent geometry : angle 0.85852 (18578) hydrogen bonds : bond 0.06036 ( 579) hydrogen bonds : angle 4.25851 ( 1804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3761.32 seconds wall clock time: 64 minutes 59.10 seconds (3899.10 seconds total)