Starting phenix.real_space_refine on Wed Mar 4 14:14:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbc_27279/03_2026/8dbc_27279.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbc_27279/03_2026/8dbc_27279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dbc_27279/03_2026/8dbc_27279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbc_27279/03_2026/8dbc_27279.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbc_27279/03_2026/8dbc_27279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbc_27279/03_2026/8dbc_27279.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.203 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 102 5.16 5 C 8892 2.51 5 N 2490 2.21 5 O 2736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14232 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "F" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "E" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 318 residue: pdb=" N HIS A 12 " occ=0.58 ... (8 atoms not shown) pdb=" NE2 HIS A 12 " occ=0.58 residue: pdb=" N ARG A 22 " occ=0.80 ... (9 atoms not shown) pdb=" NH2 ARG A 22 " occ=0.80 residue: pdb=" N GLU A 26 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 26 " occ=0.40 residue: pdb=" N LYS A 29 " occ=0.40 ... (7 atoms not shown) pdb=" NZ LYS A 29 " occ=0.40 residue: pdb=" N LYS A 33 " occ=0.01 ... (7 atoms not shown) pdb=" NZ LYS A 33 " occ=0.01 residue: pdb=" N SER A 36 " occ=0.01 ... (4 atoms not shown) pdb=" OG SER A 36 " occ=0.01 residue: pdb=" N ASN A 37 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN A 37 " occ=0.50 residue: pdb=" N CYS A 41 " occ=0.89 ... (4 atoms not shown) pdb=" SG CYS A 41 " occ=0.89 residue: pdb=" N GLU A 43 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 43 " occ=0.40 residue: pdb=" N GLU A 46 " occ=0.88 ... (7 atoms not shown) pdb=" OE2 GLU A 46 " occ=0.88 residue: pdb=" N SER A 58 " occ=0.10 ... (4 atoms not shown) pdb=" OG SER A 58 " occ=0.10 residue: pdb=" N GLY A 59 " occ=0.01 ... (2 atoms not shown) pdb=" O GLY A 59 " occ=0.01 ... (remaining 306 not shown) Time building chain proxies: 3.10, per 1000 atoms: 0.22 Number of scatterers: 14232 At special positions: 0 Unit cell: (122.515, 129.385, 79.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 102 16.00 P 12 15.00 O 2736 8.00 N 2490 7.00 C 8892 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: 1.16 Conformation dependent library (CDL) restraints added in 544.5 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 44.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 62 through 80 Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 226 through 239 Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER A 314 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 62 through 80 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 226 through 239 Processing helix chain 'B' and resid 256 through 264 Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER B 314 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 62 through 80 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 161 through 164 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 226 through 239 Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 306 Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER C 314 " --> pdb=" O TYR C 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 62 through 80 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 131 through 138 Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 161 through 164 Processing helix chain 'D' and resid 174 through 186 Processing helix chain 'D' and resid 226 through 239 Processing helix chain 'D' and resid 256 through 264 Processing helix chain 'D' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 306 Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER D 314 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 Processing helix chain 'F' and resid 62 through 80 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 131 through 138 Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 161 through 164 Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 226 through 239 Processing helix chain 'F' and resid 256 through 264 Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 306 Processing helix chain 'F' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER F 314 " --> pdb=" O TYR F 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 24 Processing helix chain 'E' and resid 62 through 80 Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 131 through 138 Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 161 through 164 Processing helix chain 'E' and resid 174 through 186 Processing helix chain 'E' and resid 226 through 239 Processing helix chain 'E' and resid 256 through 264 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 306 Processing helix chain 'E' and resid 309 through 314 removed outlier: 3.631A pdb=" N SER E 314 " --> pdb=" O TYR E 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS A 5 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 56 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 7 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 88 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS A 123 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET A 127 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 124 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU A 145 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR A 126 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 208 removed outlier: 6.745A pdb=" N MET A 222 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY A 251 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS A 250 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS B 5 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL B 56 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE B 7 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B 88 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS B 123 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET B 127 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 124 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU B 145 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR B 126 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA6, first strand: chain 'B' and resid 205 through 208 removed outlier: 6.745A pdb=" N MET B 222 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY B 251 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS B 250 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS C 5 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL C 56 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE C 7 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C 88 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS C 123 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET C 127 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 124 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU C 145 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR C 126 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 30 through 34 Processing sheet with id=AA9, first strand: chain 'C' and resid 205 through 208 removed outlier: 6.746A pdb=" N MET C 222 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY C 251 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS C 250 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS D 5 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL D 56 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE D 7 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL D 88 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS D 123 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET D 127 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE D 124 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU D 145 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB3, first strand: chain 'D' and resid 205 through 208 removed outlier: 6.746A pdb=" N MET D 222 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY D 251 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS D 250 " --> pdb=" O THR D 272 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.215A pdb=" N LYS F 5 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL F 56 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE F 7 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL F 88 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS F 123 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET F 127 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE F 124 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU F 145 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR F 126 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 30 through 34 Processing sheet with id=AB6, first strand: chain 'F' and resid 205 through 208 removed outlier: 6.746A pdb=" N MET F 222 " --> pdb=" O THR F 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY F 251 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS F 250 " --> pdb=" O THR F 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS E 5 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL E 56 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE E 7 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL E 88 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS E 123 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET E 127 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE E 124 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU E 145 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR E 126 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 30 through 34 Processing sheet with id=AB9, first strand: chain 'E' and resid 205 through 208 removed outlier: 6.745A pdb=" N MET E 222 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY E 251 " --> pdb=" O MET E 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS E 250 " --> pdb=" O THR E 272 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 1998 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4557 1.33 - 1.45: 1649 1.45 - 1.57: 8074 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 14430 Sorted by residual: bond pdb=" O4 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.568 1.497 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O4 PO4 A 402 " pdb=" P PO4 A 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PO4 E 402 " pdb=" P PO4 E 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" O2 PO4 F 402 " pdb=" P PO4 F 402 " ideal model delta sigma weight residual 1.567 1.498 0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" O2 PO4 E 402 " pdb=" P PO4 E 402 " ideal model delta sigma weight residual 1.567 1.498 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 14425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 17702 1.16 - 2.31: 1436 2.31 - 3.47: 242 3.47 - 4.63: 108 4.63 - 5.79: 36 Bond angle restraints: 19524 Sorted by residual: angle pdb=" C LEU B 27 " pdb=" N GLY B 28 " pdb=" CA GLY B 28 " ideal model delta sigma weight residual 120.10 115.71 4.39 9.50e-01 1.11e+00 2.14e+01 angle pdb=" C LEU F 27 " pdb=" N GLY F 28 " pdb=" CA GLY F 28 " ideal model delta sigma weight residual 120.10 115.72 4.38 9.50e-01 1.11e+00 2.13e+01 angle pdb=" C LEU A 27 " pdb=" N GLY A 28 " pdb=" CA GLY A 28 " ideal model delta sigma weight residual 120.10 115.73 4.37 9.50e-01 1.11e+00 2.12e+01 angle pdb=" C LEU E 27 " pdb=" N GLY E 28 " pdb=" CA GLY E 28 " ideal model delta sigma weight residual 120.10 115.73 4.37 9.50e-01 1.11e+00 2.12e+01 angle pdb=" C LEU C 27 " pdb=" N GLY C 28 " pdb=" CA GLY C 28 " ideal model delta sigma weight residual 120.10 115.73 4.37 9.50e-01 1.11e+00 2.12e+01 ... (remaining 19519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 7792 15.95 - 31.90: 716 31.90 - 47.85: 216 47.85 - 63.80: 72 63.80 - 79.75: 24 Dihedral angle restraints: 8820 sinusoidal: 3444 harmonic: 5376 Sorted by residual: dihedral pdb=" CA SER D 8 " pdb=" C SER D 8 " pdb=" N GLY D 9 " pdb=" CA GLY D 9 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER F 8 " pdb=" C SER F 8 " pdb=" N GLY F 9 " pdb=" CA GLY F 9 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER C 8 " pdb=" C SER C 8 " pdb=" N GLY C 9 " pdb=" CA GLY C 9 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 8817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1446 0.047 - 0.094: 640 0.094 - 0.141: 170 0.141 - 0.188: 36 0.188 - 0.236: 18 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CA LEU C 27 " pdb=" N LEU C 27 " pdb=" C LEU C 27 " pdb=" CB LEU C 27 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA LEU F 27 " pdb=" N LEU F 27 " pdb=" C LEU F 27 " pdb=" CB LEU F 27 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA LEU D 27 " pdb=" N LEU D 27 " pdb=" C LEU D 27 " pdb=" CB LEU D 27 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2307 not shown) Planarity restraints: 2496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 26 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLU C 26 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU C 26 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU C 27 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 26 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C GLU A 26 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU A 26 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU A 27 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 26 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C GLU E 26 " 0.062 2.00e-02 2.50e+03 pdb=" O GLU E 26 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU E 27 " -0.021 2.00e-02 2.50e+03 ... (remaining 2493 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 246 2.68 - 3.23: 13661 3.23 - 3.79: 23503 3.79 - 4.34: 31945 4.34 - 4.90: 51985 Nonbonded interactions: 121340 Sorted by model distance: nonbonded pdb=" OD2 ASP F 101 " pdb=" NZ LYS E 176 " model vdw 2.119 3.120 nonbonded pdb=" O ILE F 6 " pdb=" N GLY F 28 " model vdw 2.218 3.120 nonbonded pdb=" O ILE A 6 " pdb=" N GLY A 28 " model vdw 2.218 3.120 nonbonded pdb=" O ILE D 6 " pdb=" N GLY D 28 " model vdw 2.218 3.120 nonbonded pdb=" O ILE B 6 " pdb=" N GLY B 28 " model vdw 2.218 3.120 ... (remaining 121335 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=0.90 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.730 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 : 0.007 0.071 14430 Z= 0.373 Angle : 0.768 5.787 19524 Z= 0.485 Chirality : 0.058 0.236 2310 Planarity : 0.004 0.036 2496 Dihedral : 15.091 79.753 5316 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.74 % Allowed : 13.30 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1830 helix: 1.20 (0.21), residues: 744 sheet: 0.04 (0.25), residues: 474 loop : -0.47 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 177 TYR 0.022 0.004 TYR B 146 PHE 0.011 0.002 PHE C 189 TRP 0.013 0.003 TRP C 162 HIS 0.005 0.002 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00712 (14430) covalent geometry : angle 0.76759 (19524) hydrogen bonds : bond 0.13391 ( 714) hydrogen bonds : angle 6.14202 ( 1998) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 419 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8555 (mttp) cc_final: 0.8332 (mttt) REVERT: B 18 LYS cc_start: 0.8651 (mttp) cc_final: 0.8380 (mttt) REVERT: B 78 LYS cc_start: 0.8219 (tptm) cc_final: 0.7894 (tptt) REVERT: B 79 ILE cc_start: 0.8228 (pt) cc_final: 0.7642 (mm) REVERT: B 307 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7535 (mt-10) REVERT: C 3 ASN cc_start: 0.7729 (m-40) cc_final: 0.7320 (m110) REVERT: C 18 LYS cc_start: 0.8684 (mttp) cc_final: 0.8365 (mttt) REVERT: C 307 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7488 (mt-10) REVERT: C 314 SER cc_start: 0.5574 (OUTLIER) cc_final: 0.5213 (p) REVERT: D 3 ASN cc_start: 0.7731 (m-40) cc_final: 0.7357 (m110) REVERT: D 18 LYS cc_start: 0.8676 (mttp) cc_final: 0.8356 (mttt) REVERT: D 307 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7496 (mt-10) REVERT: D 314 SER cc_start: 0.5582 (OUTLIER) cc_final: 0.5223 (p) REVERT: F 220 ASP cc_start: 0.6786 (OUTLIER) cc_final: 0.6420 (t0) REVERT: F 311 TYR cc_start: 0.5933 (t80) cc_final: 0.5715 (t80) REVERT: E 18 LYS cc_start: 0.8658 (mttp) cc_final: 0.8389 (mttt) REVERT: E 78 LYS cc_start: 0.8291 (tptm) cc_final: 0.7926 (tptt) REVERT: E 79 ILE cc_start: 0.8243 (pt) cc_final: 0.7649 (mm) REVERT: E 307 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7493 (mt-10) outliers start: 43 outliers final: 10 residues processed: 455 average time/residue: 0.1327 time to fit residues: 84.3326 Evaluate side-chains 369 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 356 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 314 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 193 HIS A 262 ASN A 263 ASN A 305 ASN B 66 ASN B 123 HIS B 193 HIS B 305 ASN C 64 ASN C 193 HIS C 263 ASN D 64 ASN D 193 HIS D 263 ASN F 305 ASN E 66 ASN E 123 HIS E 305 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.172214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.126878 restraints weight = 14907.051| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.89 r_work: 0.3107 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 324 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14430 Z= 0.155 Angle : 0.547 7.397 19524 Z= 0.299 Chirality : 0.049 0.173 2310 Planarity : 0.003 0.029 2496 Dihedral : 5.178 44.478 1983 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.50 % Allowed : 12.53 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1830 helix: 1.34 (0.20), residues: 756 sheet: -0.22 (0.24), residues: 498 loop : -0.31 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 243 TYR 0.012 0.001 TYR F 146 PHE 0.012 0.002 PHE D 266 TRP 0.009 0.002 TRP B 162 HIS 0.006 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00351 (14430) covalent geometry : angle 0.54687 (19524) hydrogen bonds : bond 0.04100 ( 714) hydrogen bonds : angle 5.00342 ( 1998) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 348 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 18 LYS cc_start: 0.9008 (mttp) cc_final: 0.8805 (mttt) REVERT: A 31 VAL cc_start: 0.8575 (t) cc_final: 0.8323 (p) REVERT: A 52 ASP cc_start: 0.8779 (t0) cc_final: 0.8116 (m-30) REVERT: A 212 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8319 (mptt) REVERT: A 296 LEU cc_start: 0.8797 (mt) cc_final: 0.8540 (mt) REVERT: B 38 GLN cc_start: 0.8292 (mt0) cc_final: 0.8078 (mt0) REVERT: B 52 ASP cc_start: 0.8835 (t0) cc_final: 0.8256 (m-30) REVERT: B 212 LYS cc_start: 0.8663 (tttt) cc_final: 0.8303 (mptt) REVERT: B 307 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7951 (mt-10) REVERT: C 17 GLN cc_start: 0.8633 (tp40) cc_final: 0.8371 (tp-100) REVERT: C 18 LYS cc_start: 0.8922 (mttp) cc_final: 0.8625 (mttt) REVERT: C 212 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8300 (mptt) REVERT: C 243 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7385 (mtp85) REVERT: D 17 GLN cc_start: 0.8634 (tp40) cc_final: 0.8375 (tp-100) REVERT: D 18 LYS cc_start: 0.8912 (mttp) cc_final: 0.8606 (mttt) REVERT: D 212 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8293 (mptt) REVERT: D 307 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8157 (mt-10) REVERT: F 5 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8163 (mmmt) REVERT: F 220 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7371 (t0) REVERT: F 235 LYS cc_start: 0.7612 (mmtt) cc_final: 0.6991 (mmmt) REVERT: F 279 ASP cc_start: 0.7138 (t70) cc_final: 0.6886 (t0) REVERT: F 296 LEU cc_start: 0.8560 (mt) cc_final: 0.8343 (mt) REVERT: E 52 ASP cc_start: 0.8804 (t0) cc_final: 0.8245 (m-30) REVERT: E 307 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8011 (mt-10) outliers start: 55 outliers final: 23 residues processed: 393 average time/residue: 0.1333 time to fit residues: 72.7044 Evaluate side-chains 345 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 321 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 248 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 100 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 111 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 173 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 158 ASN C 158 ASN D 158 ASN F 64 ASN F 158 ASN E 66 ASN E 158 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.155413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.106162 restraints weight = 14799.163| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.02 r_work: 0.2846 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14430 Z= 0.136 Angle : 0.509 7.740 19524 Z= 0.276 Chirality : 0.047 0.170 2310 Planarity : 0.003 0.033 2496 Dihedral : 4.574 39.445 1972 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.24 % Allowed : 12.85 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.20), residues: 1830 helix: 1.68 (0.20), residues: 756 sheet: -0.46 (0.22), residues: 510 loop : -0.36 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 243 TYR 0.012 0.001 TYR F 311 PHE 0.008 0.001 PHE D 138 TRP 0.007 0.002 TRP E 162 HIS 0.004 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00310 (14430) covalent geometry : angle 0.50912 (19524) hydrogen bonds : bond 0.03767 ( 714) hydrogen bonds : angle 4.80910 ( 1998) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 344 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8932 (mttp) cc_final: 0.8707 (mttt) REVERT: A 31 VAL cc_start: 0.8722 (t) cc_final: 0.8507 (p) REVERT: A 52 ASP cc_start: 0.8742 (t0) cc_final: 0.8055 (m-30) REVERT: A 102 LYS cc_start: 0.8872 (mttt) cc_final: 0.8563 (mttm) REVERT: A 296 LEU cc_start: 0.8681 (mt) cc_final: 0.8439 (mt) REVERT: B 38 GLN cc_start: 0.8395 (mt0) cc_final: 0.8161 (mt0) REVERT: B 52 ASP cc_start: 0.8705 (t0) cc_final: 0.8139 (m-30) REVERT: B 79 ILE cc_start: 0.8488 (pt) cc_final: 0.7953 (mm) REVERT: B 212 LYS cc_start: 0.8697 (tttt) cc_final: 0.8232 (mptt) REVERT: B 243 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.7157 (mtp85) REVERT: B 267 GLU cc_start: 0.8446 (tp30) cc_final: 0.8228 (tp30) REVERT: B 278 GLU cc_start: 0.7984 (mp0) cc_final: 0.7774 (mp0) REVERT: B 282 LYS cc_start: 0.8589 (mttt) cc_final: 0.8369 (mtmm) REVERT: B 307 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8046 (mt-10) REVERT: C 11 SER cc_start: 0.8976 (p) cc_final: 0.8724 (p) REVERT: C 18 LYS cc_start: 0.8904 (mttp) cc_final: 0.8547 (mttt) REVERT: C 158 ASN cc_start: 0.8573 (m-40) cc_final: 0.8344 (m110) REVERT: C 212 LYS cc_start: 0.8684 (ttpt) cc_final: 0.8265 (mptt) REVERT: C 224 ASP cc_start: 0.8511 (t0) cc_final: 0.8289 (t0) REVERT: C 243 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7331 (mtp85) REVERT: D 11 SER cc_start: 0.8946 (p) cc_final: 0.8693 (p) REVERT: D 18 LYS cc_start: 0.8890 (mttp) cc_final: 0.8530 (mttt) REVERT: D 158 ASN cc_start: 0.8611 (m-40) cc_final: 0.8383 (m110) REVERT: D 212 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8258 (mptt) REVERT: D 243 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7325 (mtp85) REVERT: D 307 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8338 (mt-10) REVERT: F 79 ILE cc_start: 0.8514 (pt) cc_final: 0.7783 (mm) REVERT: F 235 LYS cc_start: 0.7681 (mmtt) cc_final: 0.7129 (mmmt) REVERT: F 279 ASP cc_start: 0.7331 (t70) cc_final: 0.7004 (t0) REVERT: F 296 LEU cc_start: 0.8669 (mt) cc_final: 0.8436 (mt) REVERT: E 52 ASP cc_start: 0.8703 (t0) cc_final: 0.8158 (m-30) REVERT: E 79 ILE cc_start: 0.8491 (pt) cc_final: 0.7955 (mm) REVERT: E 212 LYS cc_start: 0.8286 (mptt) cc_final: 0.7764 (tppp) REVERT: E 243 ARG cc_start: 0.7584 (mtm-85) cc_final: 0.7150 (mtp85) REVERT: E 267 GLU cc_start: 0.8431 (tp30) cc_final: 0.8219 (tp30) REVERT: E 278 GLU cc_start: 0.7933 (mp0) cc_final: 0.7716 (mp0) REVERT: E 282 LYS cc_start: 0.8611 (mttt) cc_final: 0.8388 (mtmm) REVERT: E 307 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8075 (mt-10) outliers start: 51 outliers final: 28 residues processed: 379 average time/residue: 0.1332 time to fit residues: 69.4605 Evaluate side-chains 349 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 321 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 70 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 170 optimal weight: 0.0000 chunk 161 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 HIS F 12 HIS F 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.154925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.104828 restraints weight = 14902.532| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.94 r_work: 0.2823 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14430 Z= 0.145 Angle : 0.494 7.553 19524 Z= 0.268 Chirality : 0.047 0.167 2310 Planarity : 0.003 0.036 2496 Dihedral : 4.230 31.470 1966 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.99 % Allowed : 14.44 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1830 helix: 1.79 (0.20), residues: 756 sheet: -0.57 (0.22), residues: 510 loop : -0.47 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 96 TYR 0.012 0.001 TYR F 311 PHE 0.008 0.001 PHE B 138 TRP 0.006 0.001 TRP A 162 HIS 0.007 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00334 (14430) covalent geometry : angle 0.49416 (19524) hydrogen bonds : bond 0.03649 ( 714) hydrogen bonds : angle 4.67687 ( 1998) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 322 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8456 (tp-100) REVERT: A 18 LYS cc_start: 0.8903 (mttp) cc_final: 0.8681 (mttt) REVERT: A 102 LYS cc_start: 0.9000 (mttt) cc_final: 0.8684 (mttm) REVERT: A 291 ASP cc_start: 0.8235 (t70) cc_final: 0.7924 (t0) REVERT: A 296 LEU cc_start: 0.8704 (mt) cc_final: 0.8483 (mt) REVERT: B 38 GLN cc_start: 0.8394 (mt0) cc_final: 0.8193 (mt0) REVERT: B 52 ASP cc_start: 0.8683 (t0) cc_final: 0.8105 (m-30) REVERT: B 79 ILE cc_start: 0.8363 (pt) cc_final: 0.7907 (mm) REVERT: B 212 LYS cc_start: 0.8730 (tttt) cc_final: 0.8351 (mptt) REVERT: B 243 ARG cc_start: 0.7533 (mtm-85) cc_final: 0.7205 (mtp85) REVERT: B 267 GLU cc_start: 0.8399 (tp30) cc_final: 0.8176 (tp30) REVERT: B 278 GLU cc_start: 0.7973 (mp0) cc_final: 0.7652 (mp0) REVERT: B 282 LYS cc_start: 0.8606 (mttt) cc_final: 0.8384 (mtmm) REVERT: B 307 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8000 (mt-10) REVERT: C 11 SER cc_start: 0.8973 (p) cc_final: 0.8771 (p) REVERT: C 17 GLN cc_start: 0.8628 (tp40) cc_final: 0.8384 (tp-100) REVERT: C 18 LYS cc_start: 0.8881 (mttp) cc_final: 0.8531 (mttt) REVERT: C 38 GLN cc_start: 0.8421 (mt0) cc_final: 0.8107 (mm-40) REVERT: C 212 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8269 (mptt) REVERT: C 243 ARG cc_start: 0.7625 (mtm-85) cc_final: 0.7296 (mtp85) REVERT: D 11 SER cc_start: 0.8946 (p) cc_final: 0.8741 (p) REVERT: D 17 GLN cc_start: 0.8599 (tp40) cc_final: 0.8380 (tp-100) REVERT: D 18 LYS cc_start: 0.8849 (mttp) cc_final: 0.8501 (mttt) REVERT: D 212 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8245 (mptt) REVERT: D 224 ASP cc_start: 0.8481 (t0) cc_final: 0.8156 (t0) REVERT: D 243 ARG cc_start: 0.7616 (mtm-85) cc_final: 0.7225 (mtp85) REVERT: D 307 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8319 (mt-10) REVERT: F 235 LYS cc_start: 0.7691 (mmtt) cc_final: 0.7163 (mmmt) REVERT: F 247 ILE cc_start: 0.8864 (mt) cc_final: 0.8646 (mm) REVERT: F 279 ASP cc_start: 0.7433 (t70) cc_final: 0.7053 (t0) REVERT: F 296 LEU cc_start: 0.8639 (mt) cc_final: 0.8414 (mt) REVERT: E 52 ASP cc_start: 0.8663 (t0) cc_final: 0.8097 (m-30) REVERT: E 79 ILE cc_start: 0.8382 (pt) cc_final: 0.7924 (mm) REVERT: E 243 ARG cc_start: 0.7555 (mtm-85) cc_final: 0.7193 (mtp85) REVERT: E 267 GLU cc_start: 0.8436 (tp30) cc_final: 0.8213 (tp30) REVERT: E 278 GLU cc_start: 0.8027 (mp0) cc_final: 0.7712 (mp0) REVERT: E 282 LYS cc_start: 0.8631 (mttt) cc_final: 0.8406 (mtmm) REVERT: E 307 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8009 (mt-10) outliers start: 47 outliers final: 36 residues processed: 355 average time/residue: 0.1409 time to fit residues: 68.7772 Evaluate side-chains 335 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 299 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 85 optimal weight: 0.8980 chunk 176 optimal weight: 0.3980 chunk 133 optimal weight: 0.4980 chunk 101 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN F 158 ASN F 277 GLN E 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.155085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.104842 restraints weight = 14925.581| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.93 r_work: 0.2826 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14430 Z= 0.133 Angle : 0.477 7.576 19524 Z= 0.259 Chirality : 0.047 0.164 2310 Planarity : 0.003 0.031 2496 Dihedral : 4.105 30.620 1966 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.31 % Allowed : 15.78 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.20), residues: 1830 helix: 1.89 (0.20), residues: 756 sheet: -0.59 (0.23), residues: 492 loop : -0.69 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 96 TYR 0.011 0.001 TYR F 311 PHE 0.024 0.001 PHE F 189 TRP 0.006 0.001 TRP E 162 HIS 0.007 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00305 (14430) covalent geometry : angle 0.47711 (19524) hydrogen bonds : bond 0.03457 ( 714) hydrogen bonds : angle 4.59657 ( 1998) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 314 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8676 (mt) cc_final: 0.8473 (mt) REVERT: B 52 ASP cc_start: 0.8672 (t0) cc_final: 0.8114 (m-30) REVERT: B 79 ILE cc_start: 0.8305 (pt) cc_final: 0.7894 (mm) REVERT: B 184 ARG cc_start: 0.8384 (tpp80) cc_final: 0.7863 (tpp80) REVERT: B 212 LYS cc_start: 0.8741 (tttt) cc_final: 0.8298 (mptt) REVERT: B 243 ARG cc_start: 0.7526 (mtm-85) cc_final: 0.7231 (mtp85) REVERT: B 278 GLU cc_start: 0.7964 (mp0) cc_final: 0.7653 (mp0) REVERT: B 282 LYS cc_start: 0.8623 (mttt) cc_final: 0.8410 (mtmm) REVERT: B 307 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7983 (mt-10) REVERT: C 18 LYS cc_start: 0.8846 (mttp) cc_final: 0.8494 (mttt) REVERT: C 35 PHE cc_start: 0.8146 (m-10) cc_final: 0.7946 (m-10) REVERT: C 38 GLN cc_start: 0.8391 (mt0) cc_final: 0.8114 (mm-40) REVERT: C 212 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8265 (mptt) REVERT: C 243 ARG cc_start: 0.7608 (mtm-85) cc_final: 0.7260 (mtp85) REVERT: C 279 ASP cc_start: 0.7181 (t0) cc_final: 0.6833 (t0) REVERT: D 35 PHE cc_start: 0.8150 (m-10) cc_final: 0.7921 (m-10) REVERT: D 38 GLN cc_start: 0.8443 (mt0) cc_final: 0.8179 (mm-40) REVERT: D 212 LYS cc_start: 0.8644 (ttpt) cc_final: 0.8252 (mptt) REVERT: D 222 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8076 (ptm) REVERT: D 224 ASP cc_start: 0.8373 (t0) cc_final: 0.8059 (t0) REVERT: D 307 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8325 (mt-10) REVERT: F 17 GLN cc_start: 0.8679 (tp40) cc_final: 0.8369 (tp-100) REVERT: F 279 ASP cc_start: 0.7474 (t70) cc_final: 0.7074 (t0) REVERT: E 52 ASP cc_start: 0.8686 (t0) cc_final: 0.8168 (m-30) REVERT: E 79 ILE cc_start: 0.8313 (pt) cc_final: 0.7902 (mm) REVERT: E 99 LYS cc_start: 0.7840 (pttm) cc_final: 0.7599 (pttp) REVERT: E 243 ARG cc_start: 0.7556 (mtm-85) cc_final: 0.7240 (mtp85) REVERT: E 278 GLU cc_start: 0.7996 (mp0) cc_final: 0.7685 (mp0) REVERT: E 282 LYS cc_start: 0.8638 (mttt) cc_final: 0.8431 (mtmm) REVERT: E 307 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8003 (mt-10) outliers start: 52 outliers final: 40 residues processed: 343 average time/residue: 0.1346 time to fit residues: 63.7570 Evaluate side-chains 329 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 288 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 121 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN B 263 ASN C 123 HIS ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN F 12 HIS F 123 HIS F 158 ASN F 193 HIS F 277 GLN E 193 HIS E 263 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.155179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.103311 restraints weight = 14839.506| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.99 r_work: 0.2800 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14430 Z= 0.171 Angle : 0.509 8.024 19524 Z= 0.274 Chirality : 0.047 0.165 2310 Planarity : 0.003 0.032 2496 Dihedral : 4.194 30.672 1966 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.18 % Allowed : 16.67 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1830 helix: 1.84 (0.20), residues: 756 sheet: -0.63 (0.23), residues: 492 loop : -0.73 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 96 TYR 0.010 0.001 TYR F 311 PHE 0.029 0.001 PHE A 189 TRP 0.006 0.001 TRP F 154 HIS 0.006 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00399 (14430) covalent geometry : angle 0.50917 (19524) hydrogen bonds : bond 0.03777 ( 714) hydrogen bonds : angle 4.57868 ( 1998) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 305 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 SER cc_start: 0.8610 (t) cc_final: 0.8410 (t) REVERT: A 17 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8548 (tp-100) REVERT: A 212 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8283 (mptt) REVERT: A 296 LEU cc_start: 0.8704 (mt) cc_final: 0.8476 (mt) REVERT: B 52 ASP cc_start: 0.8681 (t0) cc_final: 0.8141 (m-30) REVERT: B 79 ILE cc_start: 0.8321 (pt) cc_final: 0.7950 (mm) REVERT: B 212 LYS cc_start: 0.8768 (tttt) cc_final: 0.8151 (mmtt) REVERT: B 243 ARG cc_start: 0.7542 (mtm-85) cc_final: 0.7260 (mtp85) REVERT: B 278 GLU cc_start: 0.8072 (mp0) cc_final: 0.7775 (mp0) REVERT: B 307 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8035 (mt-10) REVERT: C 8 SER cc_start: 0.8645 (t) cc_final: 0.8418 (p) REVERT: C 35 PHE cc_start: 0.8189 (m-10) cc_final: 0.7955 (m-10) REVERT: C 38 GLN cc_start: 0.8523 (mt0) cc_final: 0.8295 (mm-40) REVERT: C 212 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8177 (mmtt) REVERT: C 243 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.7249 (mtp85) REVERT: C 279 ASP cc_start: 0.7365 (t0) cc_final: 0.7056 (t0) REVERT: D 8 SER cc_start: 0.8634 (t) cc_final: 0.8393 (p) REVERT: D 35 PHE cc_start: 0.8208 (m-10) cc_final: 0.7929 (m-10) REVERT: D 38 GLN cc_start: 0.8539 (mt0) cc_final: 0.8277 (mm-40) REVERT: D 212 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8162 (mmtt) REVERT: D 222 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8082 (ptm) REVERT: D 224 ASP cc_start: 0.8493 (t0) cc_final: 0.8217 (t0) REVERT: D 243 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7239 (mtp85) REVERT: D 307 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8358 (mt-10) REVERT: F 279 ASP cc_start: 0.7537 (t70) cc_final: 0.7117 (t0) REVERT: E 52 ASP cc_start: 0.8698 (t0) cc_final: 0.8170 (m-30) REVERT: E 79 ILE cc_start: 0.8353 (pt) cc_final: 0.7966 (mm) REVERT: E 99 LYS cc_start: 0.7915 (pttm) cc_final: 0.7676 (pttp) REVERT: E 184 ARG cc_start: 0.8347 (tpp80) cc_final: 0.7795 (tpp80) REVERT: E 243 ARG cc_start: 0.7581 (mtm-85) cc_final: 0.7267 (mtp85) REVERT: E 278 GLU cc_start: 0.8064 (mp0) cc_final: 0.7770 (mp0) outliers start: 50 outliers final: 36 residues processed: 333 average time/residue: 0.1289 time to fit residues: 59.8918 Evaluate side-chains 324 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 287 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 3 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 172 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 263 ASN B 64 ASN B 263 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN F 277 GLN ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.155970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.103901 restraints weight = 14817.148| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.01 r_work: 0.2814 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14430 Z= 0.137 Angle : 0.483 6.783 19524 Z= 0.261 Chirality : 0.046 0.166 2310 Planarity : 0.003 0.033 2496 Dihedral : 3.893 13.343 1962 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.18 % Allowed : 16.92 % Favored : 79.90 % 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: 0.53 (0.20), residues: 1830 helix: 1.92 (0.20), residues: 756 sheet: -0.66 (0.23), residues: 492 loop : -0.72 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 96 TYR 0.010 0.001 TYR F 311 PHE 0.024 0.001 PHE A 189 TRP 0.006 0.001 TRP C 162 HIS 0.006 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00316 (14430) covalent geometry : angle 0.48308 (19524) hydrogen bonds : bond 0.03418 ( 714) hydrogen bonds : angle 4.49688 ( 1998) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 288 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 212 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8170 (mmtt) REVERT: B 52 ASP cc_start: 0.8690 (t0) cc_final: 0.8170 (m-30) REVERT: B 212 LYS cc_start: 0.8778 (tttt) cc_final: 0.8170 (mmtt) REVERT: B 243 ARG cc_start: 0.7577 (mtm-85) cc_final: 0.7252 (mtp85) REVERT: B 278 GLU cc_start: 0.8056 (mp0) cc_final: 0.7756 (mp0) REVERT: C 35 PHE cc_start: 0.8243 (m-10) cc_final: 0.8002 (m-10) REVERT: C 212 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8149 (mmtt) REVERT: C 243 ARG cc_start: 0.7558 (mtm-85) cc_final: 0.7221 (mtp85) REVERT: C 279 ASP cc_start: 0.7412 (t0) cc_final: 0.7091 (t0) REVERT: D 35 PHE cc_start: 0.8206 (m-10) cc_final: 0.7983 (m-10) REVERT: D 212 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8139 (mmtt) REVERT: D 222 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8054 (ptm) REVERT: D 224 ASP cc_start: 0.8391 (t0) cc_final: 0.8143 (t0) REVERT: D 243 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.7179 (mtp85) REVERT: D 307 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8353 (mt-10) REVERT: F 17 GLN cc_start: 0.8818 (tp40) cc_final: 0.8578 (tp-100) REVERT: F 265 CYS cc_start: 0.8894 (p) cc_final: 0.8488 (p) REVERT: F 279 ASP cc_start: 0.7520 (t70) cc_final: 0.7116 (t0) REVERT: E 17 GLN cc_start: 0.8573 (tp40) cc_final: 0.8228 (tp-100) REVERT: E 52 ASP cc_start: 0.8668 (t0) cc_final: 0.8149 (m-30) REVERT: E 78 LYS cc_start: 0.8498 (tppt) cc_final: 0.8058 (tptt) REVERT: E 79 ILE cc_start: 0.8289 (pt) cc_final: 0.7915 (mm) REVERT: E 184 ARG cc_start: 0.8281 (tpp80) cc_final: 0.7720 (tpp80) REVERT: E 243 ARG cc_start: 0.7534 (mtm-85) cc_final: 0.7234 (mtp85) REVERT: E 278 GLU cc_start: 0.8083 (mp0) cc_final: 0.7789 (mp0) outliers start: 50 outliers final: 43 residues processed: 317 average time/residue: 0.1191 time to fit residues: 53.9961 Evaluate side-chains 320 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 276 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 128 optimal weight: 0.0770 chunk 17 optimal weight: 8.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 158 ASN A 263 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN F 277 GLN ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.154941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.103083 restraints weight = 14797.363| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.00 r_work: 0.2795 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14430 Z= 0.167 Angle : 0.514 8.803 19524 Z= 0.275 Chirality : 0.047 0.176 2310 Planarity : 0.003 0.038 2496 Dihedral : 3.953 14.060 1962 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.24 % Allowed : 16.67 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.20), residues: 1830 helix: 1.84 (0.20), residues: 756 sheet: -0.74 (0.23), residues: 528 loop : -1.05 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 184 TYR 0.010 0.001 TYR F 311 PHE 0.023 0.001 PHE A 189 TRP 0.006 0.001 TRP B 162 HIS 0.006 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00391 (14430) covalent geometry : angle 0.51441 (19524) hydrogen bonds : bond 0.03689 ( 714) hydrogen bonds : angle 4.53182 ( 1998) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 298 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8803 (tp-100) cc_final: 0.8596 (tp-100) REVERT: A 212 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8221 (mmtt) REVERT: A 279 ASP cc_start: 0.7294 (t0) cc_final: 0.7055 (t0) REVERT: B 17 GLN cc_start: 0.8526 (tp40) cc_final: 0.8214 (tp-100) REVERT: B 52 ASP cc_start: 0.8679 (t0) cc_final: 0.8163 (m-30) REVERT: B 79 ILE cc_start: 0.8280 (pt) cc_final: 0.7827 (mm) REVERT: B 99 LYS cc_start: 0.7985 (pttm) cc_final: 0.7708 (pttp) REVERT: B 184 ARG cc_start: 0.8268 (tpp80) cc_final: 0.7390 (ttm110) REVERT: B 212 LYS cc_start: 0.8681 (tttt) cc_final: 0.8160 (mmtt) REVERT: B 278 GLU cc_start: 0.8071 (mp0) cc_final: 0.7731 (mp0) REVERT: B 282 LYS cc_start: 0.8621 (mttt) cc_final: 0.8420 (mtmm) REVERT: C 8 SER cc_start: 0.8645 (t) cc_final: 0.8400 (p) REVERT: C 212 LYS cc_start: 0.8763 (ttpt) cc_final: 0.8167 (mmtt) REVERT: C 243 ARG cc_start: 0.7538 (mtm-85) cc_final: 0.7213 (mtp85) REVERT: C 279 ASP cc_start: 0.7391 (t0) cc_final: 0.7100 (t0) REVERT: D 8 SER cc_start: 0.8627 (t) cc_final: 0.8384 (p) REVERT: D 212 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8147 (mmtt) REVERT: D 222 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8040 (ptm) REVERT: D 243 ARG cc_start: 0.7544 (mtm-85) cc_final: 0.7178 (mtp85) REVERT: D 307 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8374 (mt-10) REVERT: F 17 GLN cc_start: 0.8775 (tp40) cc_final: 0.8528 (tp-100) REVERT: F 260 ARG cc_start: 0.7282 (mtt180) cc_final: 0.6860 (ttm110) REVERT: F 279 ASP cc_start: 0.7543 (t70) cc_final: 0.7113 (t0) REVERT: E 52 ASP cc_start: 0.8672 (t0) cc_final: 0.8158 (m-30) REVERT: E 79 ILE cc_start: 0.8366 (pt) cc_final: 0.7953 (mm) REVERT: E 184 ARG cc_start: 0.8216 (tpp80) cc_final: 0.7512 (tpp80) REVERT: E 278 GLU cc_start: 0.8088 (mp0) cc_final: 0.7775 (mp0) outliers start: 51 outliers final: 42 residues processed: 326 average time/residue: 0.1259 time to fit residues: 57.7482 Evaluate side-chains 323 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 280 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 17 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 128 optimal weight: 0.0270 chunk 172 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 153 optimal weight: 0.0270 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN F 158 ASN F 277 GLN ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.156483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.105153 restraints weight = 14792.278| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.99 r_work: 0.2833 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14430 Z= 0.120 Angle : 0.481 8.030 19524 Z= 0.259 Chirality : 0.046 0.162 2310 Planarity : 0.003 0.037 2496 Dihedral : 3.790 12.698 1962 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.99 % Allowed : 16.98 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1830 helix: 2.00 (0.20), residues: 756 sheet: -0.69 (0.23), residues: 492 loop : -0.74 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 96 TYR 0.008 0.001 TYR F 311 PHE 0.021 0.001 PHE A 189 TRP 0.007 0.001 TRP A 162 HIS 0.005 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00276 (14430) covalent geometry : angle 0.48146 (19524) hydrogen bonds : bond 0.03202 ( 714) hydrogen bonds : angle 4.43202 ( 1998) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 299 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8828 (tp-100) cc_final: 0.8594 (tp-100) REVERT: A 212 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8189 (mmtt) REVERT: A 247 ILE cc_start: 0.8868 (mt) cc_final: 0.8639 (mm) REVERT: A 279 ASP cc_start: 0.7279 (t0) cc_final: 0.7043 (t0) REVERT: B 17 GLN cc_start: 0.8531 (tp40) cc_final: 0.8184 (tp-100) REVERT: B 52 ASP cc_start: 0.8639 (t0) cc_final: 0.8164 (m-30) REVERT: B 79 ILE cc_start: 0.8212 (pt) cc_final: 0.7806 (mm) REVERT: B 99 LYS cc_start: 0.7962 (pttm) cc_final: 0.7657 (pttp) REVERT: B 122 ASP cc_start: 0.8883 (m-30) cc_final: 0.8626 (m-30) REVERT: B 184 ARG cc_start: 0.8190 (tpp80) cc_final: 0.7306 (ttm110) REVERT: B 212 LYS cc_start: 0.8646 (tttt) cc_final: 0.8116 (mmtt) REVERT: B 243 ARG cc_start: 0.7561 (mtm-85) cc_final: 0.7240 (mtp85) REVERT: C 212 LYS cc_start: 0.8719 (ttpt) cc_final: 0.8088 (mmtt) REVERT: C 243 ARG cc_start: 0.7536 (mtm-85) cc_final: 0.7211 (mtp85) REVERT: C 279 ASP cc_start: 0.7381 (t0) cc_final: 0.7058 (t0) REVERT: D 96 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7633 (mtm-85) REVERT: D 212 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8070 (mmtt) REVERT: D 222 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8078 (ptm) REVERT: D 224 ASP cc_start: 0.8137 (t0) cc_final: 0.7823 (t0) REVERT: D 243 ARG cc_start: 0.7565 (mtm-85) cc_final: 0.7173 (mtp85) REVERT: D 307 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8343 (mt-10) REVERT: F 17 GLN cc_start: 0.8800 (tp40) cc_final: 0.8522 (tp-100) REVERT: F 52 ASP cc_start: 0.8797 (t0) cc_final: 0.7984 (m-30) REVERT: F 206 VAL cc_start: 0.7560 (OUTLIER) cc_final: 0.7130 (m) REVERT: F 260 ARG cc_start: 0.7237 (mtt180) cc_final: 0.6845 (ttm110) REVERT: F 279 ASP cc_start: 0.7474 (t70) cc_final: 0.7043 (t0) REVERT: E 17 GLN cc_start: 0.8566 (tp40) cc_final: 0.8250 (tp-100) REVERT: E 52 ASP cc_start: 0.8652 (t0) cc_final: 0.8279 (m-30) REVERT: E 243 ARG cc_start: 0.7599 (mtm-85) cc_final: 0.7235 (mtp85) outliers start: 47 outliers final: 39 residues processed: 327 average time/residue: 0.1337 time to fit residues: 60.8592 Evaluate side-chains 324 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 283 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 91 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 108 optimal weight: 0.0570 chunk 20 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 80 optimal weight: 0.0070 chunk 94 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 263 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN C 17 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN F 277 GLN ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.156849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.105118 restraints weight = 14785.904| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.00 r_work: 0.2835 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14430 Z= 0.119 Angle : 0.485 7.850 19524 Z= 0.260 Chirality : 0.046 0.161 2310 Planarity : 0.003 0.042 2496 Dihedral : 3.761 13.951 1962 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.74 % Allowed : 17.43 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1830 helix: 2.03 (0.20), residues: 756 sheet: -0.64 (0.23), residues: 486 loop : -0.79 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 96 TYR 0.008 0.001 TYR F 311 PHE 0.021 0.001 PHE A 189 TRP 0.007 0.001 TRP C 162 HIS 0.006 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00276 (14430) covalent geometry : angle 0.48469 (19524) hydrogen bonds : bond 0.03167 ( 714) hydrogen bonds : angle 4.38652 ( 1998) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 294 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8541 (tp-100) REVERT: A 212 LYS cc_start: 0.8706 (ttpt) cc_final: 0.8190 (mmtt) REVERT: A 279 ASP cc_start: 0.7252 (t0) cc_final: 0.7020 (t0) REVERT: B 17 GLN cc_start: 0.8510 (tp40) cc_final: 0.8192 (tp-100) REVERT: B 38 GLN cc_start: 0.8473 (mt0) cc_final: 0.8232 (mm-40) REVERT: B 52 ASP cc_start: 0.8644 (t0) cc_final: 0.8164 (m-30) REVERT: B 79 ILE cc_start: 0.8170 (pt) cc_final: 0.7781 (mm) REVERT: B 99 LYS cc_start: 0.7957 (pttm) cc_final: 0.7654 (pttp) REVERT: B 122 ASP cc_start: 0.8898 (m-30) cc_final: 0.8644 (m-30) REVERT: B 184 ARG cc_start: 0.8165 (tpp80) cc_final: 0.7285 (ttm110) REVERT: B 212 LYS cc_start: 0.8653 (tttt) cc_final: 0.8118 (mmtt) REVERT: B 243 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.7238 (mtp85) REVERT: C 17 GLN cc_start: 0.8658 (tp-100) cc_final: 0.8440 (tp40) REVERT: C 212 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8113 (mmtt) REVERT: C 243 ARG cc_start: 0.7440 (mtm-85) cc_final: 0.7114 (mtp85) REVERT: C 279 ASP cc_start: 0.7374 (t0) cc_final: 0.7038 (t0) REVERT: D 96 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7853 (mtm-85) REVERT: D 184 ARG cc_start: 0.8348 (ttm110) cc_final: 0.8121 (ttm110) REVERT: D 212 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8079 (mmtt) REVERT: D 224 ASP cc_start: 0.8205 (t0) cc_final: 0.7952 (t0) REVERT: D 243 ARG cc_start: 0.7563 (mtm-85) cc_final: 0.7192 (mtp85) REVERT: D 307 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8317 (mt-10) REVERT: F 17 GLN cc_start: 0.8803 (tp40) cc_final: 0.8523 (tp-100) REVERT: F 206 VAL cc_start: 0.7606 (OUTLIER) cc_final: 0.7196 (m) REVERT: F 260 ARG cc_start: 0.7244 (mtt180) cc_final: 0.6882 (ttm110) REVERT: F 279 ASP cc_start: 0.7465 (t70) cc_final: 0.7039 (t0) REVERT: E 17 GLN cc_start: 0.8545 (tp40) cc_final: 0.8286 (tp-100) REVERT: E 52 ASP cc_start: 0.8645 (t0) cc_final: 0.8164 (m-30) REVERT: E 79 ILE cc_start: 0.8267 (pt) cc_final: 0.8055 (mm) REVERT: E 215 VAL cc_start: 0.8082 (t) cc_final: 0.7830 (p) REVERT: E 243 ARG cc_start: 0.7596 (mtm-85) cc_final: 0.7235 (mtp85) outliers start: 43 outliers final: 37 residues processed: 319 average time/residue: 0.1343 time to fit residues: 59.8836 Evaluate side-chains 321 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 283 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 169 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 120 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 263 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN F 158 ASN F 277 GLN ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 ASN E 263 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.155834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.104149 restraints weight = 14769.332| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.00 r_work: 0.2820 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14430 Z= 0.148 Angle : 0.499 7.839 19524 Z= 0.268 Chirality : 0.046 0.162 2310 Planarity : 0.003 0.040 2496 Dihedral : 3.852 14.455 1962 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.93 % Allowed : 17.05 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1830 helix: 1.95 (0.20), residues: 756 sheet: -0.75 (0.23), residues: 492 loop : -0.81 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 96 TYR 0.008 0.001 TYR F 311 PHE 0.020 0.001 PHE A 189 TRP 0.006 0.001 TRP C 162 HIS 0.006 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00346 (14430) covalent geometry : angle 0.49877 (19524) hydrogen bonds : bond 0.03415 ( 714) hydrogen bonds : angle 4.41384 ( 1998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3633.94 seconds wall clock time: 63 minutes 0.92 seconds (3780.92 seconds total)