Starting phenix.real_space_refine on Wed Mar 4 23:38:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whs_32510/03_2026/7whs_32510.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whs_32510/03_2026/7whs_32510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7whs_32510/03_2026/7whs_32510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whs_32510/03_2026/7whs_32510.map" model { file = "/net/cci-nas-00/data/ceres_data/7whs_32510/03_2026/7whs_32510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whs_32510/03_2026/7whs_32510.cif" } resolution = 3.1 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= 0.001 sd= 0.067 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 18 5.49 5 Mg 6 5.21 5 S 102 5.16 5 C 10968 2.51 5 N 2946 2.21 5 O 3192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17232 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2839 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} Chain breaks: 1 Chain: "B" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2839 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} Chain breaks: 1 Chain: "C" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2839 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} Chain breaks: 1 Chain: "D" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2839 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} Chain breaks: 1 Chain: "E" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2839 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} Chain breaks: 1 Chain: "F" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2839 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.24, per 1000 atoms: 0.25 Number of scatterers: 17232 At special positions: 0 Unit cell: (120.91, 118.77, 105.93, 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) S 102 16.00 P 18 15.00 Mg 6 11.99 O 3192 8.00 N 2946 7.00 C 10968 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: 1.12 Conformation dependent library (CDL) restraints added in 777.7 milliseconds 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3972 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 60 sheets defined 23.2% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 30 through 33 Processing helix chain 'A' and resid 41 through 53 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 74 through 77 Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.749A pdb=" N ALA A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.934A pdb=" N ARG A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.693A pdb=" N ALA A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 245 Proline residue: A 242 - end of helix Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'B' and resid 30 through 33 Processing helix chain 'B' and resid 41 through 53 Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 74 through 77 Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.743A pdb=" N ALA B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 189 through 194 removed outlier: 3.988A pdb=" N ARG B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 removed outlier: 3.742A pdb=" N ALA B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 245 Proline residue: B 242 - end of helix Processing helix chain 'C' and resid 22 through 27 Processing helix chain 'C' and resid 30 through 33 Processing helix chain 'C' and resid 41 through 53 Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 95 through 101 removed outlier: 3.758A pdb=" N ALA C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 189 through 194 removed outlier: 4.019A pdb=" N ARG C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.740A pdb=" N ALA C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 245 Proline residue: C 242 - end of helix Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 30 through 33 Processing helix chain 'D' and resid 41 through 53 Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 74 through 77 Processing helix chain 'D' and resid 95 through 101 removed outlier: 3.719A pdb=" N ALA D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 189 through 194 removed outlier: 3.933A pdb=" N ARG D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 removed outlier: 3.721A pdb=" N ALA D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 245 Proline residue: D 242 - end of helix Processing helix chain 'E' and resid 22 through 27 Processing helix chain 'E' and resid 30 through 33 Processing helix chain 'E' and resid 41 through 53 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 74 through 77 Processing helix chain 'E' and resid 95 through 101 removed outlier: 3.743A pdb=" N ALA E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 189 through 194 removed outlier: 3.987A pdb=" N ARG E 193 " --> pdb=" O SER E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 213 removed outlier: 3.744A pdb=" N ALA E 208 " --> pdb=" O GLU E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 245 Proline residue: E 242 - end of helix Processing helix chain 'F' and resid 22 through 27 Processing helix chain 'F' and resid 30 through 33 Processing helix chain 'F' and resid 41 through 53 Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 74 through 77 Processing helix chain 'F' and resid 95 through 101 removed outlier: 3.739A pdb=" N ALA F 99 " --> pdb=" O ALA F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 148 through 153 Processing helix chain 'F' and resid 189 through 194 removed outlier: 3.990A pdb=" N ARG F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 213 removed outlier: 3.723A pdb=" N ALA F 208 " --> pdb=" O GLU F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 245 Proline residue: F 242 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 119 through 121 Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 180 removed outlier: 4.898A pdb=" N GLN A 145 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 155 through 156 Processing sheet with id=AA6, first strand: chain 'A' and resid 268 through 269 removed outlier: 6.519A pdb=" N THR A 268 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL A 286 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET A 321 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N HIS A 338 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 273 through 275 removed outlier: 6.518A pdb=" N LEU A 274 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER A 292 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA A 309 " --> pdb=" O VAL A 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 281 removed outlier: 6.759A pdb=" N LYS A 280 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 298 " --> pdb=" O VAL A 316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 350 through 351 removed outlier: 6.570A pdb=" N GLU A 350 " --> pdb=" O VAL A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 360 through 362 removed outlier: 6.724A pdb=" N LYS A 361 " --> pdb=" O ILE A 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AB3, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AB4, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AB5, first strand: chain 'B' and resid 178 through 180 removed outlier: 4.893A pdb=" N GLN B 145 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 155 through 156 Processing sheet with id=AB7, first strand: chain 'B' and resid 268 through 269 removed outlier: 6.400A pdb=" N THR B 268 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL B 286 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ARG B 304 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET B 321 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS B 338 " --> pdb=" O LEU B 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.520A pdb=" N LEU B 274 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER B 292 " --> pdb=" O ILE B 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 280 through 281 removed outlier: 6.724A pdb=" N LYS B 280 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 298 " --> pdb=" O VAL B 316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 350 through 351 removed outlier: 6.551A pdb=" N GLU B 350 " --> pdb=" O VAL B 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.527A pdb=" N LYS B 361 " --> pdb=" O ILE B 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=AC4, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AC5, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AC6, first strand: chain 'C' and resid 178 through 180 Processing sheet with id=AC7, first strand: chain 'C' and resid 155 through 156 Processing sheet with id=AC8, first strand: chain 'C' and resid 268 through 269 removed outlier: 6.371A pdb=" N THR C 268 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL C 286 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARG C 304 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N MET C 321 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N HIS C 338 " --> pdb=" O LEU C 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 273 through 275 removed outlier: 6.529A pdb=" N LEU C 274 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER C 292 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA C 309 " --> pdb=" O VAL C 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 280 through 281 removed outlier: 6.751A pdb=" N LYS C 280 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 298 " --> pdb=" O VAL C 316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 350 through 351 removed outlier: 6.523A pdb=" N GLU C 350 " --> pdb=" O VAL C 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.697A pdb=" N LYS C 361 " --> pdb=" O ILE C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 82 through 83 Processing sheet with id=AD5, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AD6, first strand: chain 'D' and resid 119 through 121 Processing sheet with id=AD7, first strand: chain 'D' and resid 178 through 180 removed outlier: 4.866A pdb=" N GLN D 145 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 155 through 156 Processing sheet with id=AD9, first strand: chain 'D' and resid 268 through 269 removed outlier: 6.525A pdb=" N THR D 268 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL D 286 " --> pdb=" O ILE D 305 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N MET D 321 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N HIS D 338 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 273 through 275 removed outlier: 6.516A pdb=" N LEU D 274 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER D 292 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA D 309 " --> pdb=" O VAL D 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 280 through 281 removed outlier: 6.756A pdb=" N LYS D 280 " --> pdb=" O ILE D 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'D' and resid 350 through 351 removed outlier: 6.562A pdb=" N GLU D 350 " --> pdb=" O VAL D 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.723A pdb=" N LYS D 361 " --> pdb=" O ILE D 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 82 through 83 Processing sheet with id=AE6, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AE7, first strand: chain 'E' and resid 119 through 121 Processing sheet with id=AE8, first strand: chain 'E' and resid 178 through 180 removed outlier: 4.906A pdb=" N GLN E 145 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 155 through 156 Processing sheet with id=AF1, first strand: chain 'E' and resid 268 through 269 removed outlier: 6.445A pdb=" N THR E 268 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL E 286 " --> pdb=" O ILE E 305 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ARG E 304 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET E 321 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS E 338 " --> pdb=" O LEU E 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 273 through 275 removed outlier: 6.494A pdb=" N LEU E 274 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER E 292 " --> pdb=" O ILE E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 280 through 281 removed outlier: 6.760A pdb=" N LYS E 280 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL E 298 " --> pdb=" O VAL E 316 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS E 315 " --> pdb=" O ILE E 333 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'E' and resid 350 through 351 removed outlier: 6.549A pdb=" N GLU E 350 " --> pdb=" O VAL E 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'E' and resid 360 through 362 removed outlier: 6.527A pdb=" N LYS E 361 " --> pdb=" O ILE E 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 82 through 83 Processing sheet with id=AF7, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AF8, first strand: chain 'F' and resid 119 through 121 Processing sheet with id=AF9, first strand: chain 'F' and resid 178 through 180 Processing sheet with id=AG1, first strand: chain 'F' and resid 155 through 156 Processing sheet with id=AG2, first strand: chain 'F' and resid 268 through 269 removed outlier: 6.410A pdb=" N THR F 268 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL F 286 " --> pdb=" O ILE F 305 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG F 304 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N MET F 321 " --> pdb=" O ILE F 339 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N HIS F 338 " --> pdb=" O LEU F 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'F' and resid 273 through 275 removed outlier: 6.531A pdb=" N LEU F 274 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER F 292 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA F 309 " --> pdb=" O VAL F 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'F' and resid 280 through 281 removed outlier: 6.546A pdb=" N LYS F 280 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL F 298 " --> pdb=" O VAL F 316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'F' and resid 350 through 351 removed outlier: 6.504A pdb=" N GLU F 350 " --> pdb=" O VAL F 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'F' and resid 360 through 362 removed outlier: 6.649A pdb=" N LYS F 361 " --> pdb=" O ILE F 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 360 hydrogen bonds defined for protein. 990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 1.50 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: 2977 1.32 - 1.44: 4309 1.44 - 1.57: 10114 1.57 - 1.69: 30 1.69 - 1.81: 174 Bond restraints: 17604 Sorted by residual: bond pdb=" C5 GTP B 401 " pdb=" C6 GTP B 401 " ideal model delta sigma weight residual 1.390 1.466 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 GTP E 401 " pdb=" C6 GTP E 401 " ideal model delta sigma weight residual 1.390 1.466 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 GTP F 401 " pdb=" C6 GTP F 401 " ideal model delta sigma weight residual 1.390 1.466 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 GTP C 401 " pdb=" C6 GTP C 401 " ideal model delta sigma weight residual 1.390 1.465 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 GTP A 401 " pdb=" C6 GTP A 401 " ideal model delta sigma weight residual 1.390 1.465 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 17599 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 23450 2.64 - 5.29: 341 5.29 - 7.93: 66 7.93 - 10.58: 15 10.58 - 13.22: 2 Bond angle restraints: 23874 Sorted by residual: angle pdb=" N ILE C 201 " pdb=" CA ILE C 201 " pdb=" C ILE C 201 " ideal model delta sigma weight residual 109.37 96.15 13.22 1.35e+00 5.49e-01 9.59e+01 angle pdb=" N GLU F 202 " pdb=" CA GLU F 202 " pdb=" C GLU F 202 " ideal model delta sigma weight residual 111.36 118.36 -7.00 1.09e+00 8.42e-01 4.12e+01 angle pdb=" N GLU E 202 " pdb=" CA GLU E 202 " pdb=" C GLU E 202 " ideal model delta sigma weight residual 111.28 117.28 -6.00 1.09e+00 8.42e-01 3.03e+01 angle pdb=" N GLU B 202 " pdb=" CA GLU B 202 " pdb=" C GLU B 202 " ideal model delta sigma weight residual 111.36 117.29 -5.93 1.09e+00 8.42e-01 2.96e+01 angle pdb=" N SER C 200 " pdb=" CA SER C 200 " pdb=" C SER C 200 " ideal model delta sigma weight residual 107.70 118.86 -11.16 2.09e+00 2.29e-01 2.85e+01 ... (remaining 23869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 10291 34.20 - 68.40: 221 68.40 - 102.61: 6 102.61 - 136.81: 6 136.81 - 171.01: 12 Dihedral angle restraints: 10536 sinusoidal: 4332 harmonic: 6204 Sorted by residual: dihedral pdb=" C5' GTP C 401 " pdb=" O5' GTP C 401 " pdb=" PA GTP C 401 " pdb=" O3A GTP C 401 " ideal model delta sinusoidal sigma weight residual 69.27 -101.74 171.01 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' GTP F 401 " pdb=" O5' GTP F 401 " pdb=" PA GTP F 401 " pdb=" O3A GTP F 401 " ideal model delta sinusoidal sigma weight residual 69.27 -100.85 170.12 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -100.44 169.71 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 10533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2399 0.098 - 0.197: 234 0.197 - 0.295: 17 0.295 - 0.394: 0 0.394 - 0.492: 2 Chirality restraints: 2652 Sorted by residual: chirality pdb=" CA ILE C 201 " pdb=" N ILE C 201 " pdb=" C ILE C 201 " pdb=" CB ILE C 201 " both_signs ideal model delta sigma weight residual False 2.43 2.93 -0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CA GLU F 202 " pdb=" N GLU F 202 " pdb=" C GLU F 202 " pdb=" CB GLU F 202 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CA GLU C 202 " pdb=" N GLU C 202 " pdb=" C GLU C 202 " pdb=" CB GLU C 202 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 2649 not shown) Planarity restraints: 3054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 199 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ALA C 199 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA C 199 " -0.022 2.00e-02 2.50e+03 pdb=" N SER C 200 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 110 " -0.050 5.00e-02 4.00e+02 7.64e-02 9.33e+00 pdb=" N PRO B 111 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 111 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 111 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 110 " 0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO E 111 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 111 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 111 " 0.041 5.00e-02 4.00e+02 ... (remaining 3051 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1259 2.74 - 3.28: 17444 3.28 - 3.82: 28339 3.82 - 4.36: 35864 4.36 - 4.90: 61851 Nonbonded interactions: 144757 Sorted by model distance: nonbonded pdb=" OG SER B 325 " pdb=" O SER B 343 " model vdw 2.197 3.040 nonbonded pdb=" OG SER C 325 " pdb=" O SER C 343 " model vdw 2.205 3.040 nonbonded pdb=" OG SER E 325 " pdb=" O SER E 343 " model vdw 2.206 3.040 nonbonded pdb=" OG SER F 325 " pdb=" O SER F 343 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASP B 226 " pdb="MG MG B 402 " model vdw 2.217 2.170 ... (remaining 144752 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.020 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 : 0.005 0.076 17604 Z= 0.242 Angle : 0.783 13.220 23874 Z= 0.400 Chirality : 0.056 0.492 2652 Planarity : 0.006 0.076 3054 Dihedral : 16.308 171.012 6564 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.20 % Favored : 91.76 % Rotamer: Outliers : 0.33 % Allowed : 0.60 % Favored : 99.08 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.18), residues: 2172 helix: 1.02 (0.30), residues: 318 sheet: 0.22 (0.35), residues: 234 loop : -1.33 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 23 TYR 0.007 0.001 TYR C 233 PHE 0.014 0.001 PHE D 85 TRP 0.010 0.001 TRP F 149 HIS 0.009 0.002 HIS E 338 Details of bonding type rmsd covalent geometry : bond 0.00459 (17604) covalent geometry : angle 0.78335 (23874) hydrogen bonds : bond 0.17699 ( 360) hydrogen bonds : angle 7.26939 ( 990) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 228 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 187 ASN cc_start: 0.6731 (m-40) cc_final: 0.6464 (m110) REVERT: C 144 SER cc_start: 0.8463 (t) cc_final: 0.8082 (p) REVERT: C 201 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7757 (mt) REVERT: D 187 ASN cc_start: 0.6743 (m-40) cc_final: 0.6490 (m110) REVERT: F 102 ARG cc_start: 0.7791 (ptm160) cc_final: 0.7023 (ttm110) REVERT: F 144 SER cc_start: 0.8449 (t) cc_final: 0.8077 (p) outliers start: 6 outliers final: 4 residues processed: 233 average time/residue: 0.1211 time to fit residues: 43.9565 Evaluate side-chains 211 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 206 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain F residue 201 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS B 261 HIS C 107 GLN C 132 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 261 HIS F 107 GLN F 132 HIS ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.197066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.146752 restraints weight = 17130.128| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.98 r_work: 0.3420 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17604 Z= 0.129 Angle : 0.615 7.430 23874 Z= 0.308 Chirality : 0.051 0.252 2652 Planarity : 0.005 0.053 3054 Dihedral : 15.174 169.241 2440 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.71 % Allowed : 7.76 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.18), residues: 2172 helix: 0.14 (0.27), residues: 390 sheet: 0.31 (0.40), residues: 174 loop : -1.32 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 102 TYR 0.014 0.002 TYR E 152 PHE 0.011 0.001 PHE D 85 TRP 0.009 0.001 TRP A 336 HIS 0.006 0.001 HIS B 261 Details of bonding type rmsd covalent geometry : bond 0.00306 (17604) covalent geometry : angle 0.61536 (23874) hydrogen bonds : bond 0.05042 ( 360) hydrogen bonds : angle 6.35758 ( 990) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 0.470 Fit side-chains REVERT: A 187 ASN cc_start: 0.6612 (m-40) cc_final: 0.6121 (m110) REVERT: A 212 GLU cc_start: 0.6336 (tt0) cc_final: 0.5858 (tt0) REVERT: A 237 MET cc_start: 0.8454 (ttp) cc_final: 0.8048 (ttm) REVERT: B 56 GLU cc_start: 0.7799 (tp30) cc_final: 0.7493 (mm-30) REVERT: C 41 MET cc_start: 0.8117 (mtt) cc_final: 0.7846 (mtt) REVERT: C 144 SER cc_start: 0.8121 (t) cc_final: 0.7659 (p) REVERT: C 202 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6720 (pm20) REVERT: D 187 ASN cc_start: 0.6625 (m-40) cc_final: 0.6141 (m110) REVERT: D 212 GLU cc_start: 0.6303 (tt0) cc_final: 0.5888 (tt0) REVERT: D 237 MET cc_start: 0.8462 (ttp) cc_final: 0.8051 (ttm) REVERT: F 144 SER cc_start: 0.8229 (t) cc_final: 0.7870 (p) outliers start: 13 outliers final: 7 residues processed: 219 average time/residue: 0.1398 time to fit residues: 46.1995 Evaluate side-chains 204 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 153 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 0.0370 chunk 215 optimal weight: 1.9990 chunk 43 optimal weight: 0.0270 chunk 206 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS D 132 HIS ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 HIS ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.195293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.144468 restraints weight = 17263.668| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.99 r_work: 0.3390 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17604 Z= 0.138 Angle : 0.592 6.070 23874 Z= 0.296 Chirality : 0.051 0.205 2652 Planarity : 0.005 0.047 3054 Dihedral : 14.940 176.274 2438 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 1.85 % Allowed : 10.15 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.18), residues: 2172 helix: 0.24 (0.27), residues: 390 sheet: 0.38 (0.36), residues: 204 loop : -1.39 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 178 TYR 0.012 0.002 TYR B 233 PHE 0.010 0.001 PHE A 167 TRP 0.009 0.001 TRP A 336 HIS 0.008 0.001 HIS B 261 Details of bonding type rmsd covalent geometry : bond 0.00340 (17604) covalent geometry : angle 0.59216 (23874) hydrogen bonds : bond 0.04662 ( 360) hydrogen bonds : angle 6.17666 ( 990) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 VAL cc_start: 0.6346 (OUTLIER) cc_final: 0.6103 (t) REVERT: A 212 GLU cc_start: 0.6424 (tt0) cc_final: 0.6087 (tt0) REVERT: B 87 VAL cc_start: 0.6371 (OUTLIER) cc_final: 0.6129 (t) REVERT: C 41 MET cc_start: 0.8132 (mtt) cc_final: 0.7898 (mtt) REVERT: C 87 VAL cc_start: 0.6122 (OUTLIER) cc_final: 0.5885 (t) REVERT: D 87 VAL cc_start: 0.6354 (OUTLIER) cc_final: 0.6091 (t) REVERT: D 212 GLU cc_start: 0.6385 (tt0) cc_final: 0.6080 (tt0) REVERT: E 87 VAL cc_start: 0.6456 (OUTLIER) cc_final: 0.6209 (t) REVERT: F 202 GLU cc_start: 0.7494 (mp0) cc_final: 0.7061 (mp0) outliers start: 34 outliers final: 18 residues processed: 223 average time/residue: 0.1290 time to fit residues: 44.0846 Evaluate side-chains 209 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 292 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 44 optimal weight: 0.4980 chunk 204 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS B 132 HIS C 132 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 HIS D 132 HIS E 132 HIS F 132 HIS ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.189781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139002 restraints weight = 17432.613| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.75 r_work: 0.3247 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17604 Z= 0.229 Angle : 0.662 9.690 23874 Z= 0.333 Chirality : 0.054 0.173 2652 Planarity : 0.005 0.047 3054 Dihedral : 14.848 178.386 2438 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.88 % Allowed : 11.78 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.17), residues: 2172 helix: 0.22 (0.27), residues: 390 sheet: -0.30 (0.32), residues: 264 loop : -1.64 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 263 TYR 0.016 0.002 TYR C 233 PHE 0.011 0.001 PHE E 167 TRP 0.015 0.002 TRP A 336 HIS 0.026 0.002 HIS E 261 Details of bonding type rmsd covalent geometry : bond 0.00585 (17604) covalent geometry : angle 0.66154 (23874) hydrogen bonds : bond 0.05263 ( 360) hydrogen bonds : angle 6.19091 ( 990) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 195 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 VAL cc_start: 0.6188 (OUTLIER) cc_final: 0.5983 (t) REVERT: A 212 GLU cc_start: 0.6419 (tt0) cc_final: 0.6086 (tt0) REVERT: B 87 VAL cc_start: 0.6210 (OUTLIER) cc_final: 0.5972 (t) REVERT: B 201 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6938 (tt) REVERT: D 212 GLU cc_start: 0.6438 (tt0) cc_final: 0.6010 (tt0) REVERT: E 87 VAL cc_start: 0.6150 (OUTLIER) cc_final: 0.5911 (t) REVERT: E 201 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6907 (tt) REVERT: F 202 GLU cc_start: 0.7530 (mp0) cc_final: 0.6999 (mp0) outliers start: 53 outliers final: 30 residues processed: 236 average time/residue: 0.1294 time to fit residues: 46.8922 Evaluate side-chains 223 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain F residue 338 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 106 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 92 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 261 HIS B 132 HIS C 132 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS D 261 HIS E 132 HIS ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.192689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.142639 restraints weight = 17456.002| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.57 r_work: 0.3299 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17604 Z= 0.134 Angle : 0.595 7.964 23874 Z= 0.300 Chirality : 0.050 0.158 2652 Planarity : 0.005 0.048 3054 Dihedral : 14.729 179.568 2438 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.55 % Allowed : 12.60 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.17), residues: 2172 helix: 0.25 (0.27), residues: 390 sheet: -0.68 (0.35), residues: 204 loop : -1.63 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 23 TYR 0.012 0.001 TYR B 233 PHE 0.007 0.001 PHE A 167 TRP 0.009 0.001 TRP A 336 HIS 0.009 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00327 (17604) covalent geometry : angle 0.59473 (23874) hydrogen bonds : bond 0.04573 ( 360) hydrogen bonds : angle 6.07979 ( 990) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 VAL cc_start: 0.6150 (OUTLIER) cc_final: 0.5941 (t) REVERT: A 212 GLU cc_start: 0.6396 (tt0) cc_final: 0.6095 (tt0) REVERT: B 87 VAL cc_start: 0.6215 (OUTLIER) cc_final: 0.5989 (t) REVERT: B 221 GLU cc_start: 0.8014 (pm20) cc_final: 0.7385 (mm-30) REVERT: C 41 MET cc_start: 0.8085 (mtt) cc_final: 0.7753 (mtt) REVERT: D 212 GLU cc_start: 0.6382 (tt0) cc_final: 0.5993 (tt0) REVERT: D 221 GLU cc_start: 0.8030 (pm20) cc_final: 0.7418 (mm-30) REVERT: E 87 VAL cc_start: 0.6185 (OUTLIER) cc_final: 0.5956 (t) REVERT: E 201 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.7037 (tt) REVERT: F 202 GLU cc_start: 0.7570 (mp0) cc_final: 0.7016 (mp0) outliers start: 47 outliers final: 33 residues processed: 226 average time/residue: 0.1291 time to fit residues: 45.0241 Evaluate side-chains 217 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain F residue 338 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 140 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS B 132 HIS C 132 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 HIS ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.190651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.139329 restraints weight = 17411.012| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.70 r_work: 0.3265 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17604 Z= 0.183 Angle : 0.617 6.477 23874 Z= 0.309 Chirality : 0.052 0.163 2652 Planarity : 0.005 0.048 3054 Dihedral : 14.598 179.437 2436 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.71 % Allowed : 13.52 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.17), residues: 2172 helix: 0.25 (0.27), residues: 390 sheet: -0.51 (0.33), residues: 234 loop : -1.70 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 23 TYR 0.014 0.002 TYR B 233 PHE 0.011 0.001 PHE E 167 TRP 0.012 0.002 TRP A 336 HIS 0.012 0.002 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00460 (17604) covalent geometry : angle 0.61671 (23874) hydrogen bonds : bond 0.04837 ( 360) hydrogen bonds : angle 6.08073 ( 990) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 VAL cc_start: 0.6160 (OUTLIER) cc_final: 0.5958 (t) REVERT: A 212 GLU cc_start: 0.6347 (tt0) cc_final: 0.6038 (tt0) REVERT: B 87 VAL cc_start: 0.6150 (OUTLIER) cc_final: 0.5903 (t) REVERT: B 221 GLU cc_start: 0.8084 (pm20) cc_final: 0.7405 (mm-30) REVERT: D 212 GLU cc_start: 0.6313 (tt0) cc_final: 0.6021 (tt0) REVERT: D 231 LYS cc_start: 0.7810 (tttp) cc_final: 0.7079 (pttp) REVERT: E 87 VAL cc_start: 0.6132 (OUTLIER) cc_final: 0.5885 (t) REVERT: E 201 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6824 (tt) REVERT: E 266 ARG cc_start: 0.7633 (mmm-85) cc_final: 0.7384 (mmm160) outliers start: 50 outliers final: 36 residues processed: 225 average time/residue: 0.1287 time to fit residues: 44.7426 Evaluate side-chains 220 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain F residue 338 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 177 optimal weight: 0.5980 chunk 169 optimal weight: 0.3980 chunk 167 optimal weight: 0.0980 chunk 113 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS C 132 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 261 HIS F 132 HIS ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.194912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138520 restraints weight = 17243.839| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.94 r_work: 0.3392 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17604 Z= 0.107 Angle : 0.570 9.513 23874 Z= 0.286 Chirality : 0.050 0.320 2652 Planarity : 0.005 0.048 3054 Dihedral : 14.300 176.148 2436 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.88 % Allowed : 13.90 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.17), residues: 2172 helix: 0.28 (0.27), residues: 390 sheet: -0.68 (0.35), residues: 204 loop : -1.64 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 77 TYR 0.011 0.001 TYR B 233 PHE 0.010 0.001 PHE B 167 TRP 0.007 0.001 TRP F 149 HIS 0.017 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00251 (17604) covalent geometry : angle 0.57010 (23874) hydrogen bonds : bond 0.04146 ( 360) hydrogen bonds : angle 5.94845 ( 990) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 184 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 VAL cc_start: 0.6026 (OUTLIER) cc_final: 0.5782 (t) REVERT: A 212 GLU cc_start: 0.6217 (tt0) cc_final: 0.5920 (tt0) REVERT: B 87 VAL cc_start: 0.6150 (OUTLIER) cc_final: 0.5914 (t) REVERT: B 221 GLU cc_start: 0.8009 (pm20) cc_final: 0.7287 (mm-30) REVERT: D 212 GLU cc_start: 0.6229 (tt0) cc_final: 0.5956 (tt0) REVERT: D 221 GLU cc_start: 0.8004 (pm20) cc_final: 0.7416 (mm-30) REVERT: E 87 VAL cc_start: 0.6203 (OUTLIER) cc_final: 0.5972 (t) REVERT: E 201 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6740 (tt) REVERT: E 266 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7516 (mmm160) REVERT: F 202 GLU cc_start: 0.7645 (mp0) cc_final: 0.7093 (mp0) outliers start: 53 outliers final: 36 residues processed: 229 average time/residue: 0.1224 time to fit residues: 43.9257 Evaluate side-chains 222 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 292 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 292 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 59 optimal weight: 0.0030 chunk 109 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 63 optimal weight: 0.0030 chunk 210 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 67 optimal weight: 0.0570 chunk 116 optimal weight: 0.0970 overall best weight: 0.1516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS B 132 HIS B 261 HIS B 331 ASN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 ASN F 132 HIS ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.202102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.158505 restraints weight = 17512.793| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.17 r_work: 0.3471 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17604 Z= 0.095 Angle : 0.557 9.349 23874 Z= 0.280 Chirality : 0.050 0.305 2652 Planarity : 0.005 0.047 3054 Dihedral : 13.970 171.475 2436 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.55 % Allowed : 14.55 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.17), residues: 2172 helix: 0.34 (0.28), residues: 390 sheet: -0.65 (0.35), residues: 204 loop : -1.61 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 263 TYR 0.010 0.001 TYR B 233 PHE 0.010 0.001 PHE E 167 TRP 0.008 0.001 TRP F 149 HIS 0.017 0.001 HIS E 261 Details of bonding type rmsd covalent geometry : bond 0.00215 (17604) covalent geometry : angle 0.55699 (23874) hydrogen bonds : bond 0.03824 ( 360) hydrogen bonds : angle 5.80073 ( 990) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 VAL cc_start: 0.6149 (OUTLIER) cc_final: 0.5918 (t) REVERT: A 212 GLU cc_start: 0.6518 (tt0) cc_final: 0.6181 (tt0) REVERT: B 56 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7029 (mm-30) REVERT: B 87 VAL cc_start: 0.6277 (OUTLIER) cc_final: 0.6031 (t) REVERT: B 221 GLU cc_start: 0.7942 (pm20) cc_final: 0.7478 (mm-30) REVERT: D 212 GLU cc_start: 0.6496 (tt0) cc_final: 0.6285 (tt0) REVERT: D 221 GLU cc_start: 0.7924 (pm20) cc_final: 0.7493 (mm-30) REVERT: E 87 VAL cc_start: 0.6285 (OUTLIER) cc_final: 0.6036 (t) REVERT: E 201 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7630 (tt) REVERT: E 266 ARG cc_start: 0.7737 (mmm-85) cc_final: 0.7459 (mmm160) REVERT: F 144 SER cc_start: 0.8400 (t) cc_final: 0.8050 (p) REVERT: F 202 GLU cc_start: 0.7845 (mp0) cc_final: 0.7294 (mp0) outliers start: 47 outliers final: 35 residues processed: 228 average time/residue: 0.1309 time to fit residues: 45.6984 Evaluate side-chains 223 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 292 SER Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 292 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 28 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 213 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS C 132 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.194070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148518 restraints weight = 17487.291| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.45 r_work: 0.3319 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17604 Z= 0.142 Angle : 0.582 8.570 23874 Z= 0.290 Chirality : 0.052 0.330 2652 Planarity : 0.005 0.046 3054 Dihedral : 13.902 171.720 2436 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.33 % Allowed : 14.66 % Favored : 83.01 % 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: -1.59 (0.17), residues: 2172 helix: 0.34 (0.28), residues: 390 sheet: -0.43 (0.33), residues: 234 loop : -1.64 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 263 TYR 0.013 0.001 TYR B 233 PHE 0.011 0.001 PHE E 167 TRP 0.010 0.001 TRP D 336 HIS 0.017 0.002 HIS B 261 Details of bonding type rmsd covalent geometry : bond 0.00355 (17604) covalent geometry : angle 0.58217 (23874) hydrogen bonds : bond 0.04298 ( 360) hydrogen bonds : angle 5.74353 ( 990) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 VAL cc_start: 0.6252 (OUTLIER) cc_final: 0.6045 (t) REVERT: A 212 GLU cc_start: 0.6508 (tt0) cc_final: 0.6286 (tt0) REVERT: B 87 VAL cc_start: 0.6288 (OUTLIER) cc_final: 0.6054 (t) REVERT: B 221 GLU cc_start: 0.7940 (pm20) cc_final: 0.7470 (mm-30) REVERT: D 221 GLU cc_start: 0.8002 (pm20) cc_final: 0.7569 (mm-30) REVERT: E 87 VAL cc_start: 0.6080 (OUTLIER) cc_final: 0.5828 (t) REVERT: E 201 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7718 (tt) REVERT: E 266 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7665 (mmm160) REVERT: F 202 GLU cc_start: 0.7774 (mp0) cc_final: 0.7254 (mp0) outliers start: 43 outliers final: 35 residues processed: 216 average time/residue: 0.1257 time to fit residues: 41.9531 Evaluate side-chains 217 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain F residue 338 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 13 optimal weight: 0.9990 chunk 124 optimal weight: 0.0050 chunk 118 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 115 optimal weight: 0.3980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.195225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.151868 restraints weight = 17274.474| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.19 r_work: 0.3345 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17604 Z= 0.113 Angle : 0.564 8.410 23874 Z= 0.282 Chirality : 0.051 0.291 2652 Planarity : 0.005 0.046 3054 Dihedral : 13.778 169.684 2436 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.28 % Allowed : 14.77 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.17), residues: 2172 helix: 0.35 (0.28), residues: 390 sheet: -0.62 (0.35), residues: 204 loop : -1.64 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 77 TYR 0.012 0.001 TYR B 233 PHE 0.011 0.001 PHE E 167 TRP 0.007 0.001 TRP F 149 HIS 0.005 0.001 HIS B 261 Details of bonding type rmsd covalent geometry : bond 0.00274 (17604) covalent geometry : angle 0.56417 (23874) hydrogen bonds : bond 0.04074 ( 360) hydrogen bonds : angle 5.68693 ( 990) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7235 (mm-30) REVERT: B 87 VAL cc_start: 0.6157 (OUTLIER) cc_final: 0.5938 (t) REVERT: B 221 GLU cc_start: 0.7951 (pm20) cc_final: 0.7519 (mm-30) REVERT: D 221 GLU cc_start: 0.8016 (pm20) cc_final: 0.7579 (mm-30) REVERT: E 87 VAL cc_start: 0.6153 (OUTLIER) cc_final: 0.5893 (t) REVERT: E 201 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7902 (tt) REVERT: F 202 GLU cc_start: 0.7822 (mp0) cc_final: 0.7311 (mp0) outliers start: 42 outliers final: 37 residues processed: 219 average time/residue: 0.1224 time to fit residues: 41.9607 Evaluate side-chains 221 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain F residue 338 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 46 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 174 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 55 optimal weight: 0.0060 chunk 116 optimal weight: 0.0970 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 261 HIS F 132 HIS ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.196775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.153424 restraints weight = 17314.523| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.14 r_work: 0.3405 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17604 Z= 0.102 Angle : 0.556 8.056 23874 Z= 0.278 Chirality : 0.050 0.293 2652 Planarity : 0.005 0.046 3054 Dihedral : 13.612 167.050 2436 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.55 % Allowed : 14.50 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.17), residues: 2172 helix: 0.38 (0.28), residues: 390 sheet: -0.56 (0.35), residues: 204 loop : -1.63 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 263 TYR 0.011 0.001 TYR B 233 PHE 0.010 0.001 PHE B 167 TRP 0.007 0.001 TRP F 149 HIS 0.011 0.001 HIS B 261 Details of bonding type rmsd covalent geometry : bond 0.00241 (17604) covalent geometry : angle 0.55629 (23874) hydrogen bonds : bond 0.03885 ( 360) hydrogen bonds : angle 5.63045 ( 990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4112.34 seconds wall clock time: 71 minutes 4.17 seconds (4264.17 seconds total)