Starting phenix.real_space_refine on Thu Jun 12 23:59:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbg_27283/06_2025/8dbg_27283.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbg_27283/06_2025/8dbg_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_27283/06_2025/8dbg_27283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbg_27283/06_2025/8dbg_27283.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbg_27283/06_2025/8dbg_27283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbg_27283/06_2025/8dbg_27283.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.69, per 1000 atoms: 0.67 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: 3.73 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.70 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: 4.92 Time building geometry restraints manager: 4.42 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 2.590 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.140 Process input model: 36.150 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.090 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.003 TRP B 162 HIS 0.005 0.001 HIS E 130 PHE 0.011 0.002 PHE D 189 TYR 0.022 0.004 TYR D 146 ARG 0.004 0.001 ARG F 177 Details of bonding type rmsd hydrogen bonds : bond 0.13188 ( 714) hydrogen bonds : angle 6.05771 ( 1998) covalent geometry : bond 0.00687 (14628) covalent geometry : angle 0.69329 (19836) *********************** 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 : 1.639 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: 1.3074 time to fit residues: 517.6682 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 : 1.503 ------------------------------------------------------------------------------- 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 151 optimal weight: 0.9990 chunk 136 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.146229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.119540 restraints weight = 12315.830| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.03 r_work: 0.3188 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 324 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1063 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= 0.132 Angle : 0.524 6.153 19836 Z= 0.297 Chirality : 0.048 0.164 2334 Planarity : 0.003 0.022 2502 Dihedral : 13.061 86.412 2196 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.99 % Allowed : 11.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1830 helix: 1.54 (0.20), residues: 756 sheet: 0.11 (0.24), residues: 474 loop : -0.38 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 162 HIS 0.004 0.001 HIS D 130 PHE 0.009 0.001 PHE C 138 TYR 0.012 0.001 TYR C 146 ARG 0.002 0.000 ARG C 301 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 714) hydrogen bonds : angle 5.11201 ( 1998) covalent geometry : bond 0.00273 (14628) covalent geometry : angle 0.52394 (19836) *********************** 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 368 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 321 time to evaluate : 1.514 Fit side-chains REVERT: A 6 ILE cc_start: 0.9095 (mm) cc_final: 0.8853 (mm) REVERT: A 115 MET cc_start: 0.9217 (mtm) cc_final: 0.8960 (mtp) REVERT: A 279 ASP cc_start: 0.7088 (t70) cc_final: 0.6847 (t70) REVERT: A 294 MET cc_start: 0.8962 (pmm) cc_final: 0.8735 (pmm) REVERT: B 6 ILE cc_start: 0.9122 (mm) cc_final: 0.8907 (mm) REVERT: B 220 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: C 127 MET cc_start: 0.9153 (ttm) cc_final: 0.8757 (ttm) REVERT: C 178 VAL cc_start: 0.8910 (m) cc_final: 0.8687 (t) REVERT: C 263 ASN cc_start: 0.8274 (m-40) cc_final: 0.8057 (m110) REVERT: D 127 MET cc_start: 0.9157 (ttm) cc_final: 0.8766 (ttm) REVERT: D 178 VAL cc_start: 0.8921 (m) cc_final: 0.8700 (t) REVERT: D 263 ASN cc_start: 0.8272 (m-40) cc_final: 0.8049 (m110) REVERT: D 281 MET cc_start: 0.8912 (mtp) cc_final: 0.8691 (mtm) REVERT: E 6 ILE cc_start: 0.9123 (mm) cc_final: 0.8909 (mm) REVERT: E 220 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7813 (m-30) REVERT: F 6 ILE cc_start: 0.9095 (mm) cc_final: 0.8851 (mm) REVERT: F 279 ASP cc_start: 0.7094 (t70) cc_final: 0.6867 (t70) REVERT: F 294 MET cc_start: 0.8960 (pmm) cc_final: 0.8732 (pmm) outliers start: 47 outliers final: 28 residues processed: 353 average time/residue: 1.3755 time to fit residues: 528.0280 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 : 1.595 ------------------------------------------------------------------------------- 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 18 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 111 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.125786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.098940 restraints weight = 12407.808| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 0.99 r_work: 0.2893 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14628 Z= 0.217 Angle : 0.598 6.688 19836 Z= 0.338 Chirality : 0.052 0.227 2334 Planarity : 0.003 0.024 2502 Dihedral : 13.137 89.934 2184 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.54 % Allowed : 11.39 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1830 helix: 1.68 (0.20), residues: 756 sheet: -0.02 (0.24), residues: 474 loop : -0.35 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 162 HIS 0.006 0.002 HIS B 130 PHE 0.010 0.002 PHE B 189 TYR 0.016 0.002 TYR C 146 ARG 0.004 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.05590 ( 714) hydrogen bonds : angle 5.09761 ( 1998) covalent geometry : bond 0.00487 (14628) covalent geometry : angle 0.59832 (19836) *********************** 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 341 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 301 time to evaluate : 1.837 Fit side-chains REVERT: A 6 ILE cc_start: 0.9133 (mm) cc_final: 0.8922 (mm) REVERT: A 279 ASP cc_start: 0.7233 (t70) cc_final: 0.7001 (t70) REVERT: B 220 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7775 (m-30) REVERT: C 220 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: D 220 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: D 281 MET cc_start: 0.9036 (mtp) cc_final: 0.8680 (mtm) REVERT: F 6 ILE cc_start: 0.9136 (mm) cc_final: 0.8926 (mm) REVERT: F 279 ASP cc_start: 0.7282 (t70) cc_final: 0.7042 (t70) outliers start: 40 outliers final: 30 residues processed: 329 average time/residue: 1.8670 time to fit residues: 666.0699 Evaluate side-chains 326 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 293 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 178 VAL 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 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 220 ASP 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 E residue 237 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 101 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.100579 restraints weight = 12416.724| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.00 r_work: 0.2959 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 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 = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1330 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= 0.136 Angle : 0.518 5.773 19836 Z= 0.293 Chirality : 0.048 0.169 2334 Planarity : 0.003 0.022 2502 Dihedral : 11.880 82.851 2184 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.74 % Allowed : 10.94 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.20), residues: 1830 helix: 1.84 (0.20), residues: 756 sheet: -0.05 (0.24), residues: 474 loop : -0.43 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 162 HIS 0.003 0.001 HIS B 130 PHE 0.008 0.001 PHE F 189 TYR 0.013 0.002 TYR C 146 ARG 0.002 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.04574 ( 714) hydrogen bonds : angle 4.95089 ( 1998) covalent geometry : bond 0.00290 (14628) covalent geometry : angle 0.51818 (19836) *********************** 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 345 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 302 time to evaluate : 1.729 Fit side-chains REVERT: A 6 ILE cc_start: 0.9137 (mm) cc_final: 0.8902 (mm) REVERT: A 237 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7829 (tp) REVERT: A 279 ASP cc_start: 0.7267 (t70) cc_final: 0.7019 (t70) REVERT: E 188 ASP cc_start: 0.7997 (m-30) cc_final: 0.7733 (m-30) REVERT: F 6 ILE cc_start: 0.9140 (mm) cc_final: 0.8905 (mm) REVERT: F 237 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7869 (tp) REVERT: F 279 ASP cc_start: 0.7253 (t70) cc_final: 0.7019 (t70) outliers start: 43 outliers final: 30 residues processed: 334 average time/residue: 1.6809 time to fit residues: 609.4103 Evaluate side-chains 329 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 297 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 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 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 237 LEU Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 71 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 84 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 168 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.126461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.098815 restraints weight = 12481.037| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.00 r_work: 0.2909 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- 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 = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1322 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= 0.172 Angle : 0.552 6.010 19836 Z= 0.311 Chirality : 0.050 0.180 2334 Planarity : 0.003 0.022 2502 Dihedral : 12.229 87.618 2184 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.93 % Allowed : 11.01 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1830 helix: 1.87 (0.20), residues: 756 sheet: -0.25 (0.23), residues: 486 loop : -0.35 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 162 HIS 0.004 0.001 HIS E 130 PHE 0.008 0.002 PHE F 189 TYR 0.015 0.002 TYR D 146 ARG 0.003 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.05009 ( 714) hydrogen bonds : angle 4.95191 ( 1998) covalent geometry : bond 0.00379 (14628) covalent geometry : angle 0.55169 (19836) *********************** 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 342 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 296 time to evaluate : 1.509 Fit side-chains REVERT: A 6 ILE cc_start: 0.9133 (mm) cc_final: 0.8910 (mm) REVERT: B 188 ASP cc_start: 0.7972 (m-30) cc_final: 0.7703 (m-30) REVERT: C 220 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7816 (m-30) REVERT: C 260 ARG cc_start: 0.8687 (mtt180) cc_final: 0.8454 (mtt180) REVERT: D 220 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7791 (m-30) REVERT: D 281 MET cc_start: 0.8992 (mtm) cc_final: 0.8744 (mtm) REVERT: E 188 ASP cc_start: 0.7980 (m-30) cc_final: 0.7711 (m-30) REVERT: F 6 ILE cc_start: 0.9139 (mm) cc_final: 0.8915 (mm) REVERT: F 237 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7835 (tp) REVERT: F 279 ASP cc_start: 0.7267 (t70) cc_final: 0.7030 (t70) outliers start: 46 outliers final: 28 residues processed: 330 average time/residue: 1.4946 time to fit residues: 534.1845 Evaluate side-chains 321 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 54 optimal weight: 0.6980 chunk 133 optimal weight: 0.0170 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.126586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.098645 restraints weight = 12463.983| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.01 r_work: 0.2909 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 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 = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14628 Z= 0.188 Angle : 0.566 6.192 19836 Z= 0.320 Chirality : 0.051 0.219 2334 Planarity : 0.003 0.025 2502 Dihedral : 12.493 89.798 2184 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.35 % Allowed : 11.32 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1830 helix: 1.84 (0.20), residues: 756 sheet: -0.27 (0.23), residues: 486 loop : -0.35 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 154 HIS 0.004 0.001 HIS E 130 PHE 0.008 0.002 PHE F 189 TYR 0.016 0.002 TYR C 146 ARG 0.003 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.05145 ( 714) hydrogen bonds : angle 4.97415 ( 1998) covalent geometry : bond 0.00418 (14628) covalent geometry : angle 0.56646 (19836) *********************** 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 336 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 299 time to evaluate : 2.694 Fit side-chains REVERT: A 6 ILE cc_start: 0.9142 (mm) cc_final: 0.8930 (mm) REVERT: A 39 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8799 (mt-10) REVERT: A 237 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7811 (tp) REVERT: B 188 ASP cc_start: 0.7963 (m-30) cc_final: 0.7682 (m-30) REVERT: C 220 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7816 (m-30) REVERT: D 220 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7791 (m-30) REVERT: D 281 MET cc_start: 0.9022 (mtm) cc_final: 0.8773 (mtm) REVERT: E 153 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8531 (tttp) REVERT: E 188 ASP cc_start: 0.7971 (m-30) cc_final: 0.7690 (m-30) REVERT: F 6 ILE cc_start: 0.9150 (mm) cc_final: 0.8936 (mm) REVERT: F 237 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7834 (tp) REVERT: F 279 ASP cc_start: 0.7312 (t70) cc_final: 0.7078 (t70) outliers start: 37 outliers final: 27 residues processed: 327 average time/residue: 1.6352 time to fit residues: 581.6335 Evaluate side-chains 320 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 288 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 153 LYS 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 91 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.126968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.098939 restraints weight = 12487.038| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.01 r_work: 0.2918 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1379 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= 0.178 Angle : 0.557 6.086 19836 Z= 0.315 Chirality : 0.050 0.200 2334 Planarity : 0.003 0.023 2502 Dihedral : 12.476 89.525 2184 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.42 % Allowed : 11.64 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1830 helix: 1.83 (0.20), residues: 756 sheet: -0.28 (0.23), residues: 486 loop : -0.35 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 162 HIS 0.004 0.001 HIS E 130 PHE 0.007 0.002 PHE F 189 TYR 0.017 0.002 TYR D 146 ARG 0.003 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.05029 ( 714) hydrogen bonds : angle 4.96412 ( 1998) covalent geometry : bond 0.00394 (14628) covalent geometry : angle 0.55741 (19836) *********************** 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 331 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 293 time to evaluate : 1.838 Fit side-chains REVERT: A 6 ILE cc_start: 0.9139 (mm) cc_final: 0.8925 (mm) REVERT: A 237 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7794 (tp) REVERT: A 279 ASP cc_start: 0.7332 (t70) cc_final: 0.7081 (t70) REVERT: B 188 ASP cc_start: 0.7960 (m-30) cc_final: 0.7675 (m-30) REVERT: C 220 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: E 153 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8525 (tttp) REVERT: E 188 ASP cc_start: 0.7946 (m-30) cc_final: 0.7553 (m-30) REVERT: F 6 ILE cc_start: 0.9148 (mm) cc_final: 0.8932 (mm) REVERT: F 237 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7828 (tp) REVERT: F 279 ASP cc_start: 0.7287 (t70) cc_final: 0.7061 (t70) outliers start: 38 outliers final: 30 residues processed: 323 average time/residue: 1.6531 time to fit residues: 579.1976 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 : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 173 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 0.0570 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.129542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.101586 restraints weight = 12524.181| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.02 r_work: 0.2963 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 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 = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1550 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= 0.125 Angle : 0.504 5.267 19836 Z= 0.284 Chirality : 0.048 0.190 2334 Planarity : 0.003 0.022 2502 Dihedral : 11.532 82.547 2184 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.04 % Allowed : 12.40 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1830 helix: 1.97 (0.20), residues: 756 sheet: -0.20 (0.23), residues: 480 loop : -0.39 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 162 HIS 0.002 0.001 HIS C 304 PHE 0.007 0.001 PHE A 189 TYR 0.014 0.001 TYR D 146 ARG 0.002 0.000 ARG D 301 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 714) hydrogen bonds : angle 4.86193 ( 1998) covalent geometry : bond 0.00265 (14628) covalent geometry : angle 0.50362 (19836) *********************** 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 328 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 296 time to evaluate : 1.594 Fit side-chains REVERT: A 6 ILE cc_start: 0.9140 (mm) cc_final: 0.8908 (mm) REVERT: A 39 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8739 (mt-10) REVERT: A 237 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7790 (tp) REVERT: A 279 ASP cc_start: 0.7298 (t70) cc_final: 0.7061 (t70) REVERT: B 237 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7860 (tp) REVERT: C 220 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: C 237 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7740 (tp) REVERT: D 237 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7757 (tp) REVERT: D 260 ARG cc_start: 0.8669 (mtt180) cc_final: 0.8390 (mtt180) REVERT: E 153 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8506 (tttp) REVERT: E 237 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7855 (tp) REVERT: F 6 ILE cc_start: 0.9147 (mm) cc_final: 0.8913 (mm) REVERT: F 237 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7791 (tp) REVERT: F 279 ASP cc_start: 0.7228 (t70) cc_final: 0.7022 (t70) outliers start: 32 outliers final: 21 residues processed: 322 average time/residue: 1.6964 time to fit residues: 592.8381 Evaluate side-chains 314 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 285 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 62 GLU 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 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 153 LYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 97 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 120 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.127489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.099263 restraints weight = 12448.679| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.02 r_work: 0.2923 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1452 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= 0.172 Angle : 0.553 5.700 19836 Z= 0.311 Chirality : 0.050 0.189 2334 Planarity : 0.003 0.021 2502 Dihedral : 12.063 88.241 2184 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.91 % Allowed : 12.98 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1830 helix: 1.94 (0.20), residues: 756 sheet: -0.31 (0.23), residues: 486 loop : -0.37 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 154 HIS 0.004 0.001 HIS E 130 PHE 0.007 0.001 PHE A 189 TYR 0.019 0.002 TYR D 146 ARG 0.002 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.04941 ( 714) hydrogen bonds : angle 4.92001 ( 1998) covalent geometry : bond 0.00381 (14628) covalent geometry : angle 0.55261 (19836) *********************** 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: 30 poor density : 296 time to evaluate : 1.466 Fit side-chains REVERT: A 6 ILE cc_start: 0.9138 (mm) cc_final: 0.8927 (mm) REVERT: A 237 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7775 (tp) REVERT: A 279 ASP cc_start: 0.7321 (t70) cc_final: 0.7083 (t70) REVERT: B 222 MET cc_start: 0.8076 (ptp) cc_final: 0.7828 (ttm) REVERT: C 220 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7813 (m-30) REVERT: D 260 ARG cc_start: 0.8675 (mtt180) cc_final: 0.8346 (mtt180) REVERT: E 39 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8834 (mt-10) REVERT: E 222 MET cc_start: 0.8098 (ptp) cc_final: 0.7847 (ttm) REVERT: F 6 ILE cc_start: 0.9146 (mm) cc_final: 0.8931 (mm) REVERT: F 237 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7795 (tp) REVERT: F 279 ASP cc_start: 0.7234 (t70) cc_final: 0.7027 (t70) outliers start: 30 outliers final: 25 residues processed: 318 average time/residue: 1.5038 time to fit residues: 517.0065 Evaluate side-chains 325 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 62 GLU 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 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 E residue 237 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 63 optimal weight: 0.0670 chunk 176 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.128944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.100856 restraints weight = 12408.401| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.01 r_work: 0.2949 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 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 = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1529 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 : 0.518 5.197 19836 Z= 0.292 Chirality : 0.048 0.185 2334 Planarity : 0.003 0.022 2502 Dihedral : 11.623 84.055 2184 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.78 % Allowed : 12.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1830 helix: 1.96 (0.20), residues: 756 sheet: -0.31 (0.23), residues: 486 loop : -0.37 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 162 HIS 0.003 0.001 HIS A 250 PHE 0.007 0.001 PHE A 189 TYR 0.017 0.002 TYR D 146 ARG 0.002 0.000 ARG D 301 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 714) hydrogen bonds : angle 4.87011 ( 1998) covalent geometry : bond 0.00296 (14628) covalent geometry : angle 0.51777 (19836) ********************** 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: 28 poor density : 293 time to evaluate : 1.498 Fit side-chains REVERT: A 6 ILE cc_start: 0.9138 (mm) cc_final: 0.8922 (mm) REVERT: A 39 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8750 (mt-10) REVERT: A 237 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7762 (tp) REVERT: B 222 MET cc_start: 0.8002 (ptp) cc_final: 0.7743 (ttm) REVERT: B 237 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7839 (tp) REVERT: C 237 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7735 (tp) REVERT: D 237 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7766 (tp) REVERT: D 260 ARG cc_start: 0.8673 (mtt180) cc_final: 0.8354 (mtt180) REVERT: E 222 MET cc_start: 0.8042 (ptp) cc_final: 0.7779 (ttm) REVERT: E 237 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7859 (tp) REVERT: F 6 ILE cc_start: 0.9147 (mm) cc_final: 0.8930 (mm) REVERT: F 237 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7766 (tp) REVERT: F 279 ASP cc_start: 0.7223 (t70) cc_final: 0.7011 (t70) REVERT: F 281 MET cc_start: 0.8785 (mtp) cc_final: 0.8578 (mmm) outliers start: 28 outliers final: 21 residues processed: 315 average time/residue: 1.4904 time to fit residues: 508.6322 Evaluate side-chains 317 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU 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 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 E residue 237 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 57 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 134 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100628 restraints weight = 12507.916| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.01 r_work: 0.2947 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- 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 = 0.52 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 = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1533 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= 0.143 Angle : 0.525 5.219 19836 Z= 0.296 Chirality : 0.049 0.185 2334 Planarity : 0.003 0.022 2502 Dihedral : 11.586 84.153 2184 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.16 % Allowed : 12.40 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1830 helix: 1.96 (0.20), residues: 756 sheet: -0.32 (0.23), residues: 486 loop : -0.36 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 162 HIS 0.003 0.001 HIS F 193 PHE 0.007 0.001 PHE F 189 TYR 0.017 0.002 TYR D 146 ARG 0.002 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 714) hydrogen bonds : angle 4.87372 ( 1998) covalent geometry : bond 0.00308 (14628) covalent geometry : angle 0.52473 (19836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15085.74 seconds wall clock time: 263 minutes 48.07 seconds (15828.07 seconds total)