Starting phenix.real_space_refine on Wed Mar 4 15:09:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbg_27283/03_2026/8dbg_27283.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbg_27283/03_2026/8dbg_27283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dbg_27283/03_2026/8dbg_27283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbg_27283/03_2026/8dbg_27283.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbg_27283/03_2026/8dbg_27283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbg_27283/03_2026/8dbg_27283.cif" } resolution = 2.2 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= 0.300 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 12 5.21 5 S 102 5.16 5 C 8952 2.51 5 N 2520 2.21 5 O 2826 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: 14442 Number of models: 1 Model: "" Number of chains: 18 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: "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: "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: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 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: 3.02, per 1000 atoms: 0.21 Number of scatterers: 14442 At special positions: 0 Unit cell: (122.396, 129.839, 76.911, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 30 15.00 Mg 12 11.99 O 2826 8.00 N 2520 7.00 C 8952 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: 1.27 Conformation dependent library (CDL) restraints added in 531.2 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: 0.43 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: 3.667A 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: 3.667A 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: 3.668A 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: 3.668A 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 '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: 3.668A 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: 3.632A pdb=" N SER E 314 " --> pdb=" O TYR E 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: 3.668A 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: 3.631A pdb=" N SER F 314 " --> pdb=" O TYR F 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS A 5 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL A 56 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE A 7 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.135A 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: 3.558A pdb=" N HIS A 123 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.081A 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: 6.696A pdb=" N MET A 222 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 6.930A 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: 6.224A pdb=" N LYS B 5 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL B 56 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE B 7 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.464A 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: 3.558A pdb=" N HIS B 123 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET B 127 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 124 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU B 145 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.700A 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: 6.696A pdb=" N MET B 222 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 6.930A 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: 6.225A pdb=" N LYS C 5 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL C 56 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE C 7 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL C 88 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS C 123 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET C 127 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.632A 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: 6.698A 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: 6.696A pdb=" N MET C 222 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY C 251 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 4.329A 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: 6.225A pdb=" N LYS D 5 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL D 56 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE D 7 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.135A 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: 3.558A pdb=" N HIS D 123 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET D 127 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.632A 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: 6.696A pdb=" N MET D 222 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY D 251 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 4.329A 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 'E' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS E 5 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL E 56 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE E 7 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.464A 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: 3.558A pdb=" N HIS E 123 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 4.081A 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: 7.389A 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=AB5, first strand: chain 'E' and resid 30 through 34 Processing sheet with id=AB6, first strand: chain 'E' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET E 222 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY E 251 " --> pdb=" O MET E 222 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS E 250 " --> pdb=" O THR E 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS F 5 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL F 56 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE F 7 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.464A 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: 6.124A 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: 4.081A 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=AB8, first strand: chain 'F' and resid 30 through 34 Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 208 removed outlier: 6.697A pdb=" N MET F 222 " --> pdb=" O THR F 249 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY F 251 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS F 250 " --> pdb=" O THR F 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: 2.23 Time building geometry restraints manager: 1.67 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: 4701 1.33 - 1.45: 1661 1.45 - 1.57: 8086 1.57 - 1.69: 30 1.69 - 1.81: 150 Bond restraints: 14628 Sorted by residual: bond pdb=" O4 PO4 E 403 " pdb=" P PO4 E 403 " 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 A 403 " pdb=" P PO4 A 403 " 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 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" O2 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.567 1.498 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O2 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.567 1.498 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 14623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 19039 1.50 - 3.01: 644 3.01 - 4.51: 123 4.51 - 6.01: 24 6.01 - 7.51: 6 Bond angle restraints: 19836 Sorted by residual: angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 132.36 7.51 1.00e+00 1.00e+00 5.65e+01 angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 132.39 7.48 1.00e+00 1.00e+00 5.60e+01 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 132.39 7.48 1.00e+00 1.00e+00 5.59e+01 angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 132.40 7.47 1.00e+00 1.00e+00 5.58e+01 angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 132.40 7.47 1.00e+00 1.00e+00 5.58e+01 ... (remaining 19831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8016 17.95 - 35.90: 678 35.90 - 53.84: 216 53.84 - 71.79: 67 71.79 - 89.74: 47 Dihedral angle restraints: 9024 sinusoidal: 3648 harmonic: 5376 Sorted by residual: dihedral pdb=" CA SER E 8 " pdb=" C SER E 8 " pdb=" N GLY E 9 " pdb=" CA GLY E 9 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 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 180.00 160.64 19.36 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 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 9021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1304 0.040 - 0.079: 716 0.079 - 0.119: 247 0.119 - 0.158: 43 0.158 - 0.198: 24 Chirality restraints: 2334 Sorted by residual: chirality pdb=" CG LEU D 248 " pdb=" CB LEU D 248 " pdb=" CD1 LEU D 248 " pdb=" CD2 LEU D 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CG LEU E 248 " pdb=" CB LEU E 248 " pdb=" CD1 LEU E 248 " pdb=" CD2 LEU E 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" CG LEU B 248 " pdb=" CB LEU B 248 " pdb=" CD1 LEU B 248 " pdb=" CD2 LEU B 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.19 2.00e-01 2.50e+01 9.50e-01 ... (remaining 2331 not shown) Planarity restraints: 2502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 180 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C SER F 180 " 0.029 2.00e-02 2.50e+03 pdb=" O SER F 180 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE F 181 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 180 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C SER A 180 " -0.029 2.00e-02 2.50e+03 pdb=" O SER A 180 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 181 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 180 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.84e+00 pdb=" C SER C 180 " -0.029 2.00e-02 2.50e+03 pdb=" O SER C 180 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE C 181 " 0.010 2.00e-02 2.50e+03 ... (remaining 2499 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 114 2.55 - 3.13: 11505 3.13 - 3.72: 23613 3.72 - 4.31: 33275 4.31 - 4.90: 55499 Nonbonded interactions: 124006 Sorted by model distance: nonbonded pdb="MG MG D 404 " pdb=" O HOH D 501 " model vdw 1.958 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH B 501 " model vdw 1.959 2.170 nonbonded pdb="MG MG F 404 " pdb=" O HOH F 501 " model vdw 1.959 2.170 nonbonded pdb="MG MG A 404 " pdb=" O HOH A 501 " model vdw 1.959 2.170 nonbonded pdb="MG MG E 404 " pdb=" O HOH E 501 " model vdw 1.959 2.170 ... (remaining 124001 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 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=0.91 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.990 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 0.070 14628 Z= 0.321 Angle : 0.693 7.513 19836 Z= 0.437 Chirality : 0.054 0.198 2334 Planarity : 0.003 0.019 2502 Dihedral : 17.531 89.739 5520 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.97 % Allowed : 12.53 % Favored : 85.50 % 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: 0.54 (0.20), residues: 1830 helix: 1.27 (0.20), residues: 744 sheet: 0.06 (0.25), residues: 474 loop : -0.38 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 177 TYR 0.022 0.004 TYR D 146 PHE 0.011 0.002 PHE D 189 TRP 0.012 0.003 TRP B 162 HIS 0.005 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00687 (14628) covalent geometry : angle 0.69329 (19836) hydrogen bonds : bond 0.13188 ( 714) hydrogen bonds : angle 6.05771 ( 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 370 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 339 time to evaluate : 0.584 Fit side-chains REVERT: A 6 ILE cc_start: 0.9058 (mm) cc_final: 0.8813 (mm) REVERT: A 294 MET cc_start: 0.8704 (pmm) cc_final: 0.8435 (pmm) REVERT: C 127 MET cc_start: 0.8754 (ttm) cc_final: 0.8254 (ttm) REVERT: D 127 MET cc_start: 0.8752 (ttm) cc_final: 0.8256 (ttm) REVERT: F 6 ILE cc_start: 0.9058 (mm) cc_final: 0.8811 (mm) REVERT: F 294 MET cc_start: 0.8718 (pmm) cc_final: 0.8453 (pmm) outliers start: 31 outliers final: 24 residues processed: 362 average time/residue: 0.5909 time to fit residues: 234.2753 Evaluate side-chains 306 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 282 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F 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: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN C 135 GLN C 305 ASN D 38 GLN D 135 GLN D 305 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.146010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.119367 restraints weight = 12328.224| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.03 r_work: 0.3185 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 324 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14628 Z= 0.138 Angle : 0.529 6.187 19836 Z= 0.300 Chirality : 0.048 0.166 2334 Planarity : 0.003 0.023 2502 Dihedral : 12.887 88.183 2196 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.99 % Allowed : 11.20 % Favored : 85.81 % 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: 0.77 (0.20), residues: 1830 helix: 1.55 (0.20), residues: 756 sheet: 0.11 (0.24), residues: 474 loop : -0.36 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 301 TYR 0.012 0.002 TYR C 146 PHE 0.010 0.001 PHE D 138 TRP 0.009 0.002 TRP B 162 HIS 0.004 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00289 (14628) covalent geometry : angle 0.52899 (19836) hydrogen bonds : bond 0.04722 ( 714) hydrogen bonds : angle 5.09999 ( 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 365 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 318 time to evaluate : 0.574 Fit side-chains REVERT: A 6 ILE cc_start: 0.9104 (mm) cc_final: 0.8853 (mm) REVERT: A 115 MET cc_start: 0.9230 (mtm) cc_final: 0.8975 (mtp) REVERT: A 294 MET cc_start: 0.8951 (pmm) cc_final: 0.8723 (pmm) REVERT: B 220 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7799 (m-30) REVERT: C 127 MET cc_start: 0.9151 (ttm) cc_final: 0.8756 (ttm) REVERT: C 178 VAL cc_start: 0.8915 (m) cc_final: 0.8674 (t) REVERT: D 127 MET cc_start: 0.9161 (ttm) cc_final: 0.8769 (ttm) REVERT: D 178 VAL cc_start: 0.8932 (m) cc_final: 0.8694 (t) REVERT: D 263 ASN cc_start: 0.8271 (m-40) cc_final: 0.8052 (m110) REVERT: E 220 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: F 6 ILE cc_start: 0.9103 (mm) cc_final: 0.8850 (mm) REVERT: F 279 ASP cc_start: 0.7085 (t70) cc_final: 0.6854 (t70) REVERT: F 294 MET cc_start: 0.8956 (pmm) cc_final: 0.8726 (pmm) outliers start: 47 outliers final: 28 residues processed: 350 average time/residue: 0.6455 time to fit residues: 245.7698 Evaluate side-chains 325 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 295 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 122 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 chunk 140 optimal weight: 0.0070 chunk 115 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.128201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.101267 restraints weight = 12500.390| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.00 r_work: 0.2950 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14628 Z= 0.146 Angle : 0.528 5.858 19836 Z= 0.299 Chirality : 0.049 0.170 2334 Planarity : 0.003 0.022 2502 Dihedral : 11.842 82.206 2184 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.86 % Allowed : 10.88 % Favored : 86.26 % 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: 0.87 (0.20), residues: 1830 helix: 1.80 (0.20), residues: 756 sheet: -0.03 (0.24), residues: 474 loop : -0.38 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 49 TYR 0.013 0.002 TYR D 146 PHE 0.008 0.001 PHE F 189 TRP 0.007 0.002 TRP B 162 HIS 0.004 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00314 (14628) covalent geometry : angle 0.52806 (19836) hydrogen bonds : bond 0.04790 ( 714) hydrogen bonds : angle 4.98575 ( 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 342 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 297 time to evaluate : 0.539 Fit side-chains REVERT: A 6 ILE cc_start: 0.9126 (mm) cc_final: 0.8892 (mm) REVERT: A 279 ASP cc_start: 0.7196 (t70) cc_final: 0.6966 (t70) REVERT: A 294 MET cc_start: 0.8904 (pmm) cc_final: 0.8633 (pmm) REVERT: C 178 VAL cc_start: 0.8916 (m) cc_final: 0.8673 (t) REVERT: C 220 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7818 (m-30) REVERT: D 178 VAL cc_start: 0.8924 (m) cc_final: 0.8682 (t) REVERT: F 6 ILE cc_start: 0.9128 (mm) cc_final: 0.8895 (mm) REVERT: F 279 ASP cc_start: 0.7238 (t70) cc_final: 0.7001 (t70) REVERT: F 294 MET cc_start: 0.8898 (pmm) cc_final: 0.8623 (pmm) outliers start: 45 outliers final: 36 residues processed: 329 average time/residue: 0.6650 time to fit residues: 237.0824 Evaluate side-chains 320 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 283 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 167 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.099959 restraints weight = 12444.465| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.00 r_work: 0.2926 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14628 Z= 0.153 Angle : 0.530 5.780 19836 Z= 0.300 Chirality : 0.049 0.169 2334 Planarity : 0.003 0.022 2502 Dihedral : 11.787 82.789 2184 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.74 % Allowed : 10.88 % Favored : 86.39 % 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: 0.91 (0.20), residues: 1830 helix: 1.88 (0.20), residues: 756 sheet: -0.08 (0.24), residues: 474 loop : -0.37 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 49 TYR 0.014 0.002 TYR C 146 PHE 0.007 0.001 PHE A 189 TRP 0.007 0.002 TRP A 162 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00332 (14628) covalent geometry : angle 0.52988 (19836) hydrogen bonds : bond 0.04785 ( 714) hydrogen bonds : angle 4.93562 ( 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 344 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 301 time to evaluate : 0.497 Fit side-chains REVERT: A 6 ILE cc_start: 0.9131 (mm) cc_final: 0.8902 (mm) REVERT: A 237 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7813 (tp) REVERT: A 279 ASP cc_start: 0.7234 (t70) cc_final: 0.6990 (t70) REVERT: A 294 MET cc_start: 0.8936 (pmm) cc_final: 0.8660 (pmm) REVERT: B 188 ASP cc_start: 0.7973 (m-30) cc_final: 0.7702 (m-30) REVERT: C 178 VAL cc_start: 0.8889 (m) cc_final: 0.8644 (t) REVERT: C 220 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: D 178 VAL cc_start: 0.8904 (m) cc_final: 0.8667 (t) REVERT: D 220 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: E 188 ASP cc_start: 0.7991 (m-30) cc_final: 0.7727 (m-30) REVERT: F 6 ILE cc_start: 0.9129 (mm) cc_final: 0.8898 (mm) REVERT: F 237 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7814 (tp) REVERT: F 279 ASP cc_start: 0.7247 (t70) cc_final: 0.7005 (t70) REVERT: F 294 MET cc_start: 0.8933 (pmm) cc_final: 0.8640 (pmm) outliers start: 43 outliers final: 32 residues processed: 334 average time/residue: 0.6468 time to fit residues: 234.2745 Evaluate side-chains 328 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 237 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 104 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.128611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.101159 restraints weight = 12552.244| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.00 r_work: 0.2957 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14628 Z= 0.133 Angle : 0.506 5.304 19836 Z= 0.286 Chirality : 0.048 0.168 2334 Planarity : 0.003 0.021 2502 Dihedral : 11.404 80.149 2184 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.12 % Allowed : 10.69 % Favored : 86.20 % 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: 0.95 (0.20), residues: 1830 helix: 1.95 (0.20), residues: 756 sheet: -0.10 (0.24), residues: 474 loop : -0.35 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 49 TYR 0.013 0.002 TYR C 146 PHE 0.007 0.001 PHE B 189 TRP 0.007 0.002 TRP A 162 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00282 (14628) covalent geometry : angle 0.50589 (19836) hydrogen bonds : bond 0.04436 ( 714) hydrogen bonds : angle 4.86823 ( 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 349 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 300 time to evaluate : 0.633 Fit side-chains REVERT: A 6 ILE cc_start: 0.9130 (mm) cc_final: 0.8899 (mm) REVERT: A 237 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7817 (tp) REVERT: A 294 MET cc_start: 0.8943 (pmm) cc_final: 0.8652 (pmm) REVERT: B 188 ASP cc_start: 0.7949 (m-30) cc_final: 0.7679 (m-30) REVERT: C 237 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7761 (tp) REVERT: C 260 ARG cc_start: 0.8681 (mtt180) cc_final: 0.8348 (mtt180) REVERT: E 39 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8780 (mt-10) REVERT: E 153 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8504 (tttp) REVERT: E 188 ASP cc_start: 0.7977 (m-30) cc_final: 0.7714 (m-30) REVERT: F 6 ILE cc_start: 0.9138 (mm) cc_final: 0.8907 (mm) REVERT: F 237 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7826 (tp) REVERT: F 279 ASP cc_start: 0.7231 (t70) cc_final: 0.7008 (t70) REVERT: F 294 MET cc_start: 0.8937 (pmm) cc_final: 0.8643 (pmm) outliers start: 49 outliers final: 27 residues processed: 337 average time/residue: 0.6810 time to fit residues: 248.6693 Evaluate side-chains 322 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 291 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 32 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.098926 restraints weight = 12465.574| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.02 r_work: 0.2907 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14628 Z= 0.186 Angle : 0.561 5.979 19836 Z= 0.316 Chirality : 0.050 0.232 2334 Planarity : 0.003 0.022 2502 Dihedral : 12.049 87.978 2180 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.16 % Allowed : 11.58 % Favored : 86.26 % 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: 0.92 (0.20), residues: 1830 helix: 1.93 (0.20), residues: 756 sheet: -0.14 (0.24), residues: 474 loop : -0.36 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.016 0.002 TYR D 146 PHE 0.008 0.002 PHE F 189 TRP 0.006 0.002 TRP B 162 HIS 0.004 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00412 (14628) covalent geometry : angle 0.56073 (19836) hydrogen bonds : bond 0.05104 ( 714) hydrogen bonds : angle 4.94068 ( 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 335 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 301 time to evaluate : 0.524 Fit side-chains REVERT: A 6 ILE cc_start: 0.9139 (mm) cc_final: 0.8939 (mm) REVERT: A 237 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7790 (tp) REVERT: A 279 ASP cc_start: 0.7281 (t70) cc_final: 0.7053 (t70) REVERT: B 188 ASP cc_start: 0.7967 (m-30) cc_final: 0.7687 (m-30) REVERT: C 220 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: E 39 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8837 (mt-10) REVERT: F 6 ILE cc_start: 0.9141 (mm) cc_final: 0.8920 (mm) REVERT: F 237 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7810 (tp) REVERT: F 279 ASP cc_start: 0.7271 (t70) cc_final: 0.7042 (t70) outliers start: 34 outliers final: 27 residues processed: 323 average time/residue: 0.6940 time to fit residues: 241.9523 Evaluate side-chains 331 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 301 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 282 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 46 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.128738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.100768 restraints weight = 12462.944| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.01 r_work: 0.2946 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14628 Z= 0.140 Angle : 0.516 5.305 19836 Z= 0.291 Chirality : 0.049 0.200 2334 Planarity : 0.003 0.020 2502 Dihedral : 11.514 83.234 2180 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.42 % Allowed : 11.77 % Favored : 85.81 % 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: 0.96 (0.20), residues: 1830 helix: 1.96 (0.20), residues: 756 sheet: -0.11 (0.24), residues: 456 loop : -0.33 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.015 0.002 TYR D 146 PHE 0.008 0.001 PHE F 189 TRP 0.008 0.002 TRP A 162 HIS 0.003 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00302 (14628) covalent geometry : angle 0.51623 (19836) hydrogen bonds : bond 0.04523 ( 714) hydrogen bonds : angle 4.88251 ( 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 335 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 297 time to evaluate : 0.505 Fit side-chains REVERT: A 6 ILE cc_start: 0.9137 (mm) cc_final: 0.8912 (mm) REVERT: A 237 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7786 (tp) REVERT: B 188 ASP cc_start: 0.7931 (m-30) cc_final: 0.7667 (m-30) REVERT: C 220 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7798 (m-30) REVERT: C 237 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7753 (tp) REVERT: C 260 ARG cc_start: 0.8681 (mtt180) cc_final: 0.8372 (mtt180) REVERT: D 237 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7754 (tp) REVERT: D 260 ARG cc_start: 0.8677 (mtt180) cc_final: 0.8363 (mtt180) REVERT: E 39 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8727 (mt-10) REVERT: E 153 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8519 (tttp) REVERT: F 6 ILE cc_start: 0.9135 (mm) cc_final: 0.8910 (mm) REVERT: F 237 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7797 (tp) REVERT: F 279 ASP cc_start: 0.7236 (t70) cc_final: 0.7015 (t70) outliers start: 38 outliers final: 30 residues processed: 323 average time/residue: 0.7135 time to fit residues: 248.6742 Evaluate side-chains 324 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 282 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 6 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.098937 restraints weight = 12403.528| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.02 r_work: 0.2919 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14628 Z= 0.186 Angle : 0.563 5.871 19836 Z= 0.317 Chirality : 0.050 0.205 2334 Planarity : 0.003 0.022 2502 Dihedral : 12.135 89.734 2180 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.29 % Allowed : 12.21 % Favored : 85.50 % 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: 0.88 (0.20), residues: 1830 helix: 1.91 (0.20), residues: 756 sheet: -0.15 (0.23), residues: 474 loop : -0.42 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.019 0.002 TYR D 146 PHE 0.008 0.002 PHE F 189 TRP 0.006 0.002 TRP B 154 HIS 0.004 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00413 (14628) covalent geometry : angle 0.56268 (19836) hydrogen bonds : bond 0.05101 ( 714) hydrogen bonds : angle 4.94094 ( 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 338 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 302 time to evaluate : 0.466 Fit side-chains REVERT: A 6 ILE cc_start: 0.9146 (mm) cc_final: 0.8940 (mm) REVERT: A 237 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7815 (tp) REVERT: A 279 ASP cc_start: 0.7261 (t70) cc_final: 0.7040 (t70) REVERT: B 188 ASP cc_start: 0.7969 (m-30) cc_final: 0.7684 (m-30) REVERT: C 220 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: D 220 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7799 (m-30) REVERT: F 6 ILE cc_start: 0.9146 (mm) cc_final: 0.8940 (mm) REVERT: F 237 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7795 (tp) REVERT: F 279 ASP cc_start: 0.7250 (t70) cc_final: 0.7030 (t70) outliers start: 36 outliers final: 30 residues processed: 326 average time/residue: 0.7177 time to fit residues: 252.0727 Evaluate side-chains 334 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 300 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 282 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 89 optimal weight: 0.1980 chunk 109 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 55 optimal weight: 0.0670 chunk 67 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.103013 restraints weight = 12613.464| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.02 r_work: 0.2984 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14628 Z= 0.113 Angle : 0.487 5.568 19836 Z= 0.274 Chirality : 0.047 0.179 2334 Planarity : 0.002 0.022 2502 Dihedral : 11.097 80.071 2180 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.04 % Allowed : 12.34 % Favored : 85.62 % 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: 0.98 (0.20), residues: 1830 helix: 2.02 (0.20), residues: 756 sheet: -0.11 (0.24), residues: 456 loop : -0.37 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 301 TYR 0.014 0.001 TYR D 146 PHE 0.007 0.001 PHE F 189 TRP 0.009 0.002 TRP A 162 HIS 0.003 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00234 (14628) covalent geometry : angle 0.48712 (19836) hydrogen bonds : bond 0.04021 ( 714) hydrogen bonds : angle 4.81949 ( 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 326 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 294 time to evaluate : 0.518 Fit side-chains REVERT: A 6 ILE cc_start: 0.9132 (mm) cc_final: 0.8908 (mm) REVERT: A 115 MET cc_start: 0.9206 (mtm) cc_final: 0.8997 (mtp) REVERT: A 237 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7835 (tp) REVERT: C 237 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7745 (tp) REVERT: C 260 ARG cc_start: 0.8680 (mtt180) cc_final: 0.8430 (mtt180) REVERT: D 237 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7765 (tp) REVERT: D 260 ARG cc_start: 0.8699 (mtt180) cc_final: 0.8451 (mtt180) REVERT: E 222 MET cc_start: 0.7958 (ptp) cc_final: 0.7698 (ttm) REVERT: F 6 ILE cc_start: 0.9130 (mm) cc_final: 0.8904 (mm) REVERT: F 237 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7825 (tp) outliers start: 32 outliers final: 23 residues processed: 319 average time/residue: 0.6973 time to fit residues: 240.4156 Evaluate side-chains 306 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 279 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 47 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN C 135 GLN D 17 GLN D 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100623 restraints weight = 12499.924| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.00 r_work: 0.2943 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14628 Z= 0.149 Angle : 0.526 5.091 19836 Z= 0.296 Chirality : 0.049 0.169 2334 Planarity : 0.003 0.021 2502 Dihedral : 11.403 83.482 2180 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.59 % Allowed : 13.04 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.20), residues: 1830 helix: 2.01 (0.20), residues: 756 sheet: -0.15 (0.24), residues: 456 loop : -0.38 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 49 TYR 0.017 0.002 TYR D 146 PHE 0.007 0.001 PHE A 189 TRP 0.007 0.002 TRP A 162 HIS 0.003 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00323 (14628) covalent geometry : angle 0.52555 (19836) hydrogen bonds : bond 0.04605 ( 714) hydrogen bonds : angle 4.86331 ( 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 321 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 296 time to evaluate : 0.571 Fit side-chains REVERT: A 6 ILE cc_start: 0.9142 (mm) cc_final: 0.8919 (mm) REVERT: A 237 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7798 (tp) REVERT: B 222 MET cc_start: 0.8101 (ptp) cc_final: 0.7839 (ttm) REVERT: C 237 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7735 (tp) REVERT: C 260 ARG cc_start: 0.8663 (mtt180) cc_final: 0.8377 (mtt180) REVERT: D 237 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7748 (tp) REVERT: D 260 ARG cc_start: 0.8662 (mtt180) cc_final: 0.8377 (mtt180) REVERT: E 222 MET cc_start: 0.8093 (ptp) cc_final: 0.7838 (ttm) REVERT: F 6 ILE cc_start: 0.9138 (mm) cc_final: 0.8916 (mm) REVERT: F 237 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7807 (tp) REVERT: F 279 ASP cc_start: 0.7207 (t70) cc_final: 0.6998 (t70) outliers start: 25 outliers final: 21 residues processed: 315 average time/residue: 0.7102 time to fit residues: 241.4607 Evaluate side-chains 311 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 286 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 96 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.101068 restraints weight = 12502.520| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.02 r_work: 0.2954 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14628 Z= 0.140 Angle : 0.517 5.040 19836 Z= 0.291 Chirality : 0.048 0.177 2334 Planarity : 0.003 0.021 2502 Dihedral : 11.285 82.381 2180 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.72 % Allowed : 13.04 % Favored : 85.24 % 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: 0.95 (0.20), residues: 1830 helix: 1.98 (0.20), residues: 756 sheet: -0.12 (0.24), residues: 456 loop : -0.38 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.017 0.002 TYR D 146 PHE 0.007 0.001 PHE F 189 TRP 0.007 0.002 TRP A 162 HIS 0.003 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00300 (14628) covalent geometry : angle 0.51700 (19836) hydrogen bonds : bond 0.04467 ( 714) hydrogen bonds : angle 4.84810 ( 1998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6654.59 seconds wall clock time: 113 minutes 38.66 seconds (6818.66 seconds total)