Starting phenix.real_space_refine on Sat Aug 23 14:46:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vuw_43542/08_2025/8vuw_43542_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vuw_43542/08_2025/8vuw_43542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vuw_43542/08_2025/8vuw_43542_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vuw_43542/08_2025/8vuw_43542_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vuw_43542/08_2025/8vuw_43542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vuw_43542/08_2025/8vuw_43542.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 30 5.16 5 C 8545 2.51 5 N 2130 2.21 5 O 2345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13055 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} Conformer: "B" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} bond proxies already assigned to first conformer: 2607 Chain: "B" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} Conformer: "B" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} bond proxies already assigned to first conformer: 2607 Chain: "C" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} Conformer: "B" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} bond proxies already assigned to first conformer: 2607 Chain: "D" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} Conformer: "B" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} bond proxies already assigned to first conformer: 2607 Chain: "E" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} Conformer: "B" Number of residues, atoms: 311, 2547 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 13, 'TRANS': 297} bond proxies already assigned to first conformer: 2607 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 106 Unusual residues: {'DHL': 1, 'PGW': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'DHL': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AGLN A 233 " occ=0.60 ... (16 atoms not shown) pdb=" NE2BGLN A 233 " occ=0.40 residue: pdb=" N AGLN B 233 " occ=0.60 ... (16 atoms not shown) pdb=" NE2BGLN B 233 " occ=0.40 residue: pdb=" N AGLN C 233 " occ=0.60 ... (16 atoms not shown) pdb=" NE2BGLN C 233 " occ=0.40 residue: pdb=" N AGLN D 233 " occ=0.60 ... (16 atoms not shown) pdb=" NE2BGLN D 233 " occ=0.40 residue: pdb=" N AGLN E 233 " occ=0.60 ... (16 atoms not shown) pdb=" NE2BGLN E 233 " occ=0.40 Time building chain proxies: 5.00, per 1000 atoms: 0.38 Number of scatterers: 13055 At special positions: 0 Unit cell: (89.723, 91.885, 123.234, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 5 15.00 O 2345 8.00 N 2130 7.00 C 8545 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: 0.89 Conformation dependent library (CDL) restraints added in 783.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2950 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 15 sheets defined 37.8% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.730A pdb=" N LEU A 232 " --> pdb=" O PHE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 Processing helix chain 'A' and resid 247 through 253 removed outlier: 3.550A pdb=" N ASN A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 287 removed outlier: 3.561A pdb=" N GLN A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 302 through 321 removed outlier: 3.913A pdb=" N LEU A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 222 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.731A pdb=" N LEU B 232 " --> pdb=" O PHE B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 Processing helix chain 'B' and resid 247 through 253 removed outlier: 3.550A pdb=" N ASN B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 287 removed outlier: 3.561A pdb=" N GLN B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 300 Processing helix chain 'B' and resid 302 through 321 removed outlier: 3.913A pdb=" N LEU B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 222 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.731A pdb=" N LEU C 232 " --> pdb=" O PHE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 244 Processing helix chain 'C' and resid 247 through 253 removed outlier: 3.550A pdb=" N ASN C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 287 removed outlier: 3.561A pdb=" N GLN C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 300 Processing helix chain 'C' and resid 302 through 321 removed outlier: 3.913A pdb=" N LEU C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG C 318 " --> pdb=" O VAL C 314 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 70 Processing helix chain 'D' and resid 176 through 179 Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 222 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.730A pdb=" N LEU D 232 " --> pdb=" O PHE D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 244 Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.550A pdb=" N ASN D 251 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 287 removed outlier: 3.561A pdb=" N GLN D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 300 Processing helix chain 'D' and resid 302 through 321 removed outlier: 3.913A pdb=" N LEU D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 176 through 179 Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 222 Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.730A pdb=" N LEU E 232 " --> pdb=" O PHE E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 244 Processing helix chain 'E' and resid 247 through 253 removed outlier: 3.550A pdb=" N ASN E 251 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 287 removed outlier: 3.561A pdb=" N GLN E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 300 Processing helix chain 'E' and resid 302 through 321 removed outlier: 3.912A pdb=" N LEU E 306 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.210A pdb=" N SER A 109 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N SER A 84 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU A 107 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP A 86 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG A 105 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLY A 88 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N ASN A 103 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N LYS A 90 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N ILE A 101 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU A 92 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N ARG A 99 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL A 12 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N SER A 143 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL A 14 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 145 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 16 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL A 147 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 18 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 58 removed outlier: 4.209A pdb=" N SER B 109 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N SER B 84 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU B 107 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 86 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG B 105 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLY B 88 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N ASN B 103 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N LYS B 90 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N ILE B 101 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU B 92 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N ARG B 99 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL B 12 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N SER B 143 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL B 14 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE B 145 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 16 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL B 147 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 18 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58 removed outlier: 4.209A pdb=" N SER C 109 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N SER C 84 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU C 107 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP C 86 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG C 105 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLY C 88 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N ASN C 103 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N LYS C 90 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N ILE C 101 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU C 92 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N ARG C 99 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL C 12 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N SER C 143 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL C 14 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE C 145 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 16 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL C 147 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 18 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.210A pdb=" N SER D 109 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER D 84 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU D 107 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP D 86 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG D 105 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLY D 88 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N ASN D 103 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N LYS D 90 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N ILE D 101 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU D 92 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N ARG D 99 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL D 12 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N SER D 143 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL D 14 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE D 145 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL D 16 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL D 147 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE D 18 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.622A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.622A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 58 removed outlier: 4.210A pdb=" N SER E 109 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N SER E 84 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU E 107 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP E 86 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG E 105 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N GLY E 88 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N ASN E 103 " --> pdb=" O GLY E 88 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N LYS E 90 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N ILE E 101 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU E 92 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N ARG E 99 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL E 12 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N SER E 143 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL E 14 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE E 145 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL E 16 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL E 147 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE E 18 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.621A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1800 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: 1.63 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2045 1.31 - 1.43: 3925 1.43 - 1.56: 7370 1.56 - 1.69: 10 1.69 - 1.81: 50 Bond restraints: 13400 Sorted by residual: bond pdb=" C1 PGW D 401 " pdb=" O01 PGW D 401 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1 PGW B 401 " pdb=" O01 PGW B 401 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 PGW C 401 " pdb=" O01 PGW C 401 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 PGW A 401 " pdb=" O01 PGW A 401 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 PGW A 403 " pdb=" O01 PGW A 403 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 13395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 17466 2.18 - 4.37: 579 4.37 - 6.55: 80 6.55 - 8.73: 40 8.73 - 10.92: 20 Bond angle restraints: 18185 Sorted by residual: angle pdb=" N THR B 234 " pdb=" CA THR B 234 " pdb=" C THR B 234 " ideal model delta sigma weight residual 111.07 106.93 4.14 1.07e+00 8.73e-01 1.49e+01 angle pdb=" N THR C 234 " pdb=" CA THR C 234 " pdb=" C THR C 234 " ideal model delta sigma weight residual 111.07 106.94 4.13 1.07e+00 8.73e-01 1.49e+01 angle pdb=" N THR E 234 " pdb=" CA THR E 234 " pdb=" C THR E 234 " ideal model delta sigma weight residual 111.07 106.94 4.13 1.07e+00 8.73e-01 1.49e+01 angle pdb=" N THR A 234 " pdb=" CA THR A 234 " pdb=" C THR A 234 " ideal model delta sigma weight residual 111.07 106.95 4.12 1.07e+00 8.73e-01 1.48e+01 angle pdb=" N THR D 234 " pdb=" CA THR D 234 " pdb=" C THR D 234 " ideal model delta sigma weight residual 111.07 106.97 4.10 1.07e+00 8.73e-01 1.46e+01 ... (remaining 18180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.37: 7505 27.37 - 54.75: 300 54.75 - 82.12: 65 82.12 - 109.49: 10 109.49 - 136.86: 15 Dihedral angle restraints: 7895 sinusoidal: 3315 harmonic: 4580 Sorted by residual: dihedral pdb=" C03 PGW C 401 " pdb=" C01 PGW C 401 " pdb=" C02 PGW C 401 " pdb=" O03 PGW C 401 " ideal model delta sinusoidal sigma weight residual -64.65 72.21 -136.86 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C03 PGW D 401 " pdb=" C01 PGW D 401 " pdb=" C02 PGW D 401 " pdb=" O03 PGW D 401 " ideal model delta sinusoidal sigma weight residual -64.65 72.20 -136.85 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" C03 PGW A 401 " pdb=" C01 PGW A 401 " pdb=" C02 PGW A 401 " pdb=" O03 PGW A 401 " ideal model delta sinusoidal sigma weight residual -64.65 72.19 -136.84 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 7892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1269 0.046 - 0.092: 486 0.092 - 0.138: 187 0.138 - 0.183: 23 0.183 - 0.229: 15 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CB VAL D 222 " pdb=" CA VAL D 222 " pdb=" CG1 VAL D 222 " pdb=" CG2 VAL D 222 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL C 222 " pdb=" CA VAL C 222 " pdb=" CG1 VAL C 222 " pdb=" CG2 VAL C 222 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL B 222 " pdb=" CA VAL B 222 " pdb=" CG1 VAL B 222 " pdb=" CG2 VAL B 222 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1977 not shown) Planarity restraints: 2300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 50 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO C 51 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 51 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 51 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 50 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO D 51 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 51 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 51 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 50 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.23e+00 pdb=" N PRO E 51 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 51 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 51 " -0.021 5.00e-02 4.00e+02 ... (remaining 2297 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3539 2.80 - 3.33: 11312 3.33 - 3.85: 22408 3.85 - 4.38: 26884 4.38 - 4.90: 46014 Nonbonded interactions: 110157 Sorted by model distance: nonbonded pdb=" ND2 ASN B 68 " pdb=" NE2 GLN C 62 " model vdw 2.280 3.200 nonbonded pdb=" OD1 ASN C 154 " pdb=" NH1 ARG C 163 " model vdw 2.284 3.120 nonbonded pdb=" OD1 ASN E 154 " pdb=" NH1 ARG E 163 " model vdw 2.285 3.120 nonbonded pdb=" ND2 ASN C 68 " pdb=" NE2 GLN D 62 " model vdw 2.285 3.200 nonbonded pdb=" OD1 ASN B 154 " pdb=" NH1 ARG B 163 " model vdw 2.285 3.120 ... (remaining 110152 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 232 or resid 234 through 321)) selection = (chain 'B' and (resid 11 through 232 or resid 234 through 321)) selection = (chain 'C' and (resid 11 through 232 or resid 234 through 321)) selection = (chain 'D' and (resid 11 through 232 or resid 234 through 321)) selection = (chain 'E' and (resid 11 through 232 or resid 234 through 321)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.350 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 0.085 13400 Z= 0.311 Angle : 0.979 10.917 18185 Z= 0.464 Chirality : 0.056 0.229 1980 Planarity : 0.005 0.038 2300 Dihedral : 17.622 136.865 4945 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.20), residues: 1560 helix: -1.44 (0.18), residues: 570 sheet: 0.07 (0.23), residues: 465 loop : -2.08 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 163 TYR 0.015 0.002 TYR E 245 PHE 0.017 0.003 PHE D 223 TRP 0.019 0.002 TRP D 161 HIS 0.004 0.002 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00680 (13400) covalent geometry : angle 0.97882 (18185) hydrogen bonds : bond 0.12095 ( 575) hydrogen bonds : angle 6.19211 ( 1800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.445 Fit side-chains REVERT: A 161 TRP cc_start: 0.8276 (m-10) cc_final: 0.7986 (m-90) REVERT: A 208 PHE cc_start: 0.8572 (t80) cc_final: 0.8349 (t80) REVERT: B 251 ASN cc_start: 0.8334 (m110) cc_final: 0.8068 (m110) REVERT: C 173 ILE cc_start: 0.8963 (mm) cc_final: 0.8733 (mm) REVERT: D 148 TYR cc_start: 0.8167 (m-80) cc_final: 0.7640 (m-80) REVERT: E 90 LYS cc_start: 0.8645 (pttp) cc_final: 0.8440 (pttp) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.0923 time to fit residues: 30.4996 Evaluate side-chains 172 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 89 ASN B 68 ASN C 68 ASN C 251 ASN D 68 ASN D 233 GLN B E 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.147003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.110100 restraints weight = 46576.032| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.68 r_work: 0.2856 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13400 Z= 0.216 Angle : 0.637 6.862 18185 Z= 0.320 Chirality : 0.048 0.158 1980 Planarity : 0.004 0.035 2300 Dihedral : 15.770 142.417 1965 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.86 % Allowed : 4.44 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.21), residues: 1560 helix: -0.19 (0.22), residues: 585 sheet: -0.10 (0.23), residues: 470 loop : -2.07 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 163 TYR 0.013 0.002 TYR A 204 PHE 0.014 0.002 PHE B 121 TRP 0.023 0.002 TRP E 161 HIS 0.002 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00508 (13400) covalent geometry : angle 0.63709 (18185) hydrogen bonds : bond 0.03535 ( 575) hydrogen bonds : angle 4.92035 ( 1800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 0.394 Fit side-chains REVERT: A 54 LYS cc_start: 0.8245 (mmtm) cc_final: 0.7632 (mtpt) REVERT: A 68 ASN cc_start: 0.8188 (m-40) cc_final: 0.7982 (m-40) REVERT: A 224 TRP cc_start: 0.7503 (m100) cc_final: 0.7225 (m100) REVERT: B 251 ASN cc_start: 0.8588 (m110) cc_final: 0.8217 (m110) REVERT: C 54 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7468 (mtpt) REVERT: D 148 TYR cc_start: 0.8588 (m-80) cc_final: 0.7846 (m-80) REVERT: D 265 MET cc_start: 0.8192 (ttm) cc_final: 0.7920 (ttm) REVERT: E 68 ASN cc_start: 0.8040 (m-40) cc_final: 0.7528 (m-40) REVERT: E 251 ASN cc_start: 0.8790 (m110) cc_final: 0.8363 (m-40) outliers start: 7 outliers final: 2 residues processed: 185 average time/residue: 0.0873 time to fit residues: 24.2675 Evaluate side-chains 162 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 136 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 116 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 60 ASN B 89 ASN D 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.152402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.121811 restraints weight = 45047.411| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.57 r_work: 0.2909 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13400 Z= 0.145 Angle : 0.560 8.136 18185 Z= 0.279 Chirality : 0.045 0.141 1980 Planarity : 0.003 0.022 2300 Dihedral : 14.671 140.412 1965 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.00 % Allowed : 5.88 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.22), residues: 1560 helix: 0.51 (0.23), residues: 555 sheet: -0.03 (0.24), residues: 435 loop : -1.93 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 163 TYR 0.009 0.001 TYR A 204 PHE 0.015 0.001 PHE A 228 TRP 0.021 0.001 TRP E 161 HIS 0.001 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00334 (13400) covalent geometry : angle 0.56049 (18185) hydrogen bonds : bond 0.02824 ( 575) hydrogen bonds : angle 4.64085 ( 1800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 0.343 Fit side-chains REVERT: A 54 LYS cc_start: 0.8158 (mmtm) cc_final: 0.7624 (mtpt) REVERT: A 224 TRP cc_start: 0.7568 (m100) cc_final: 0.7343 (m100) REVERT: B 251 ASN cc_start: 0.8525 (m110) cc_final: 0.8202 (m110) REVERT: D 148 TYR cc_start: 0.8564 (m-80) cc_final: 0.7985 (m-80) REVERT: D 224 TRP cc_start: 0.7549 (m100) cc_final: 0.7307 (m100) REVERT: D 265 MET cc_start: 0.8143 (ttm) cc_final: 0.7830 (ttm) REVERT: E 68 ASN cc_start: 0.8218 (m-40) cc_final: 0.7923 (m-40) REVERT: E 114 MET cc_start: 0.8945 (mtt) cc_final: 0.8479 (mtt) REVERT: E 251 ASN cc_start: 0.8749 (m110) cc_final: 0.8382 (m-40) outliers start: 9 outliers final: 5 residues processed: 174 average time/residue: 0.0908 time to fit residues: 23.9665 Evaluate side-chains 158 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 153 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 98 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 0.0670 chunk 91 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.152232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.115657 restraints weight = 45633.074| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.48 r_work: 0.2932 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 13400 Z= 0.109 Angle : 0.519 7.532 18185 Z= 0.258 Chirality : 0.044 0.131 1980 Planarity : 0.003 0.020 2300 Dihedral : 14.182 138.361 1965 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.00 % Allowed : 6.59 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.22), residues: 1560 helix: 0.74 (0.24), residues: 555 sheet: -0.02 (0.24), residues: 435 loop : -1.92 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 163 TYR 0.007 0.001 TYR D 203 PHE 0.023 0.001 PHE E 228 TRP 0.019 0.001 TRP E 161 HIS 0.001 0.000 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00241 (13400) covalent geometry : angle 0.51938 (18185) hydrogen bonds : bond 0.02482 ( 575) hydrogen bonds : angle 4.44202 ( 1800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 0.400 Fit side-chains REVERT: A 54 LYS cc_start: 0.7863 (mmtm) cc_final: 0.7496 (mtpt) REVERT: A 224 TRP cc_start: 0.7396 (m100) cc_final: 0.7183 (m100) REVERT: B 251 ASN cc_start: 0.8435 (m110) cc_final: 0.8137 (m110) REVERT: C 54 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7445 (mtpt) REVERT: D 148 TYR cc_start: 0.8350 (m-80) cc_final: 0.7866 (m-80) REVERT: D 265 MET cc_start: 0.8172 (ttm) cc_final: 0.7847 (ttm) REVERT: E 68 ASN cc_start: 0.8066 (m-40) cc_final: 0.7696 (m-40) REVERT: E 114 MET cc_start: 0.8870 (mtt) cc_final: 0.8410 (mtt) REVERT: E 251 ASN cc_start: 0.8645 (m110) cc_final: 0.8209 (m-40) REVERT: E 265 MET cc_start: 0.8002 (ttt) cc_final: 0.7651 (ttm) outliers start: 9 outliers final: 5 residues processed: 177 average time/residue: 0.0887 time to fit residues: 23.8088 Evaluate side-chains 162 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 2 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 117 optimal weight: 0.4980 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN B 60 ASN C 264 GLN D 60 ASN E 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.145659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.109086 restraints weight = 47505.042| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.62 r_work: 0.2833 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13400 Z= 0.225 Angle : 0.603 6.902 18185 Z= 0.305 Chirality : 0.047 0.155 1980 Planarity : 0.003 0.028 2300 Dihedral : 14.587 139.861 1965 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.22 % Allowed : 7.03 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.22), residues: 1560 helix: 0.72 (0.24), residues: 555 sheet: -0.21 (0.24), residues: 435 loop : -1.95 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 163 TYR 0.014 0.002 TYR A 204 PHE 0.029 0.002 PHE E 228 TRP 0.018 0.002 TRP E 161 HIS 0.002 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00532 (13400) covalent geometry : angle 0.60304 (18185) hydrogen bonds : bond 0.03198 ( 575) hydrogen bonds : angle 4.72469 ( 1800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.499 Fit side-chains REVERT: B 251 ASN cc_start: 0.8625 (m110) cc_final: 0.8265 (m110) REVERT: C 97 ASP cc_start: 0.8278 (p0) cc_final: 0.7854 (p0) REVERT: D 148 TYR cc_start: 0.8634 (m-80) cc_final: 0.7967 (m-80) REVERT: E 114 MET cc_start: 0.8934 (mtt) cc_final: 0.8477 (mtt) outliers start: 12 outliers final: 8 residues processed: 160 average time/residue: 0.0873 time to fit residues: 20.9296 Evaluate side-chains 155 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 95 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN C 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.149577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.113641 restraints weight = 42241.567| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.32 r_work: 0.2907 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13400 Z= 0.124 Angle : 0.530 7.405 18185 Z= 0.264 Chirality : 0.044 0.137 1980 Planarity : 0.003 0.022 2300 Dihedral : 14.177 137.968 1965 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.15 % Allowed : 7.53 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.22), residues: 1560 helix: 0.78 (0.23), residues: 555 sheet: -0.22 (0.24), residues: 435 loop : -1.96 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 163 TYR 0.007 0.001 TYR A 204 PHE 0.024 0.001 PHE E 228 TRP 0.017 0.001 TRP E 161 HIS 0.001 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00282 (13400) covalent geometry : angle 0.53012 (18185) hydrogen bonds : bond 0.02579 ( 575) hydrogen bonds : angle 4.51862 ( 1800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.302 Fit side-chains REVERT: A 54 LYS cc_start: 0.7888 (mmtm) cc_final: 0.7309 (mtpt) REVERT: B 30 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.6947 (tt0) REVERT: C 97 ASP cc_start: 0.8285 (p0) cc_final: 0.7862 (p0) REVERT: D 148 TYR cc_start: 0.8504 (m-80) cc_final: 0.7962 (m-80) REVERT: E 114 MET cc_start: 0.8897 (mtt) cc_final: 0.8437 (mtt) outliers start: 11 outliers final: 7 residues processed: 163 average time/residue: 0.0835 time to fit residues: 20.8396 Evaluate side-chains 163 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 18 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 128 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 0.0000 chunk 16 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN D 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.151264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.114896 restraints weight = 46205.756| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.46 r_work: 0.2928 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13400 Z= 0.113 Angle : 0.517 7.488 18185 Z= 0.258 Chirality : 0.044 0.130 1980 Planarity : 0.003 0.022 2300 Dihedral : 13.803 135.578 1965 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.15 % Allowed : 8.17 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.22), residues: 1560 helix: 0.90 (0.24), residues: 555 sheet: -0.10 (0.24), residues: 435 loop : -1.89 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 163 TYR 0.007 0.001 TYR D 203 PHE 0.025 0.001 PHE E 228 TRP 0.015 0.001 TRP E 161 HIS 0.002 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00256 (13400) covalent geometry : angle 0.51717 (18185) hydrogen bonds : bond 0.02480 ( 575) hydrogen bonds : angle 4.38536 ( 1800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.477 Fit side-chains REVERT: A 54 LYS cc_start: 0.7814 (mmtm) cc_final: 0.7363 (mtpt) REVERT: B 30 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6800 (tt0) REVERT: B 251 ASN cc_start: 0.8521 (m110) cc_final: 0.8238 (m110) REVERT: C 54 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7507 (mtpt) REVERT: C 97 ASP cc_start: 0.8269 (p0) cc_final: 0.7892 (p0) REVERT: C 155 GLU cc_start: 0.8025 (tt0) cc_final: 0.7407 (mt-10) REVERT: C 200 ASN cc_start: 0.8563 (t0) cc_final: 0.8284 (t0) REVERT: E 114 MET cc_start: 0.8901 (mtt) cc_final: 0.8447 (mtt) REVERT: E 265 MET cc_start: 0.8040 (ttt) cc_final: 0.7727 (ttm) outliers start: 11 outliers final: 8 residues processed: 161 average time/residue: 0.0824 time to fit residues: 20.3774 Evaluate side-chains 159 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.149649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.117755 restraints weight = 39359.337| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.90 r_work: 0.2900 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13400 Z= 0.186 Angle : 0.572 7.269 18185 Z= 0.289 Chirality : 0.046 0.142 1980 Planarity : 0.003 0.028 2300 Dihedral : 14.071 135.997 1965 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.22 % Allowed : 8.32 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.22), residues: 1560 helix: 0.87 (0.23), residues: 555 sheet: -0.23 (0.24), residues: 435 loop : -1.91 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 163 TYR 0.012 0.002 TYR A 204 PHE 0.029 0.002 PHE E 228 TRP 0.017 0.002 TRP E 161 HIS 0.002 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00440 (13400) covalent geometry : angle 0.57210 (18185) hydrogen bonds : bond 0.02946 ( 575) hydrogen bonds : angle 4.60143 ( 1800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.453 Fit side-chains REVERT: A 54 LYS cc_start: 0.7932 (mmtm) cc_final: 0.7432 (mtpt) REVERT: B 30 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7096 (tt0) REVERT: C 200 ASN cc_start: 0.8586 (t0) cc_final: 0.8255 (t0) REVERT: D 148 TYR cc_start: 0.8556 (m-80) cc_final: 0.7990 (m-80) REVERT: E 114 MET cc_start: 0.8911 (mtt) cc_final: 0.8450 (mtt) outliers start: 12 outliers final: 10 residues processed: 150 average time/residue: 0.0861 time to fit residues: 19.7978 Evaluate side-chains 155 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 60 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.144682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.109041 restraints weight = 38244.312| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.21 r_work: 0.2837 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13400 Z= 0.223 Angle : 0.609 7.194 18185 Z= 0.309 Chirality : 0.047 0.152 1980 Planarity : 0.003 0.029 2300 Dihedral : 14.386 137.307 1965 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.29 % Allowed : 8.67 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.22), residues: 1560 helix: 0.76 (0.23), residues: 555 sheet: -0.35 (0.24), residues: 435 loop : -1.98 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 163 TYR 0.014 0.002 TYR A 204 PHE 0.030 0.002 PHE C 228 TRP 0.016 0.002 TRP E 206 HIS 0.003 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00533 (13400) covalent geometry : angle 0.60939 (18185) hydrogen bonds : bond 0.03162 ( 575) hydrogen bonds : angle 4.75440 ( 1800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.378 Fit side-chains REVERT: A 54 LYS cc_start: 0.8203 (mmtm) cc_final: 0.7674 (mtpt) REVERT: B 30 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: D 148 TYR cc_start: 0.8645 (m-80) cc_final: 0.7985 (m-80) outliers start: 13 outliers final: 9 residues processed: 160 average time/residue: 0.0981 time to fit residues: 23.5911 Evaluate side-chains 155 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 91 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 110 optimal weight: 0.0980 chunk 148 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 8 optimal weight: 0.4980 chunk 78 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.150736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.115327 restraints weight = 39820.775| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.22 r_work: 0.2939 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 13400 Z= 0.109 Angle : 0.524 8.048 18185 Z= 0.261 Chirality : 0.044 0.132 1980 Planarity : 0.003 0.022 2300 Dihedral : 13.716 134.417 1965 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.22 % Allowed : 8.89 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.22), residues: 1560 helix: 0.88 (0.23), residues: 555 sheet: -0.26 (0.24), residues: 435 loop : -1.93 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 163 TYR 0.007 0.001 TYR C 203 PHE 0.022 0.001 PHE E 228 TRP 0.016 0.002 TRP E 161 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00241 (13400) covalent geometry : angle 0.52363 (18185) hydrogen bonds : bond 0.02463 ( 575) hydrogen bonds : angle 4.48703 ( 1800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.453 Fit side-chains REVERT: A 54 LYS cc_start: 0.7871 (mmtm) cc_final: 0.7380 (mtpt) REVERT: B 30 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6775 (tt0) REVERT: C 155 GLU cc_start: 0.7960 (tt0) cc_final: 0.7307 (mt-10) REVERT: D 148 TYR cc_start: 0.8418 (m-80) cc_final: 0.7888 (m-80) REVERT: E 114 MET cc_start: 0.8868 (mtt) cc_final: 0.8401 (mtt) REVERT: E 172 ASP cc_start: 0.7670 (m-30) cc_final: 0.7383 (m-30) outliers start: 12 outliers final: 9 residues processed: 152 average time/residue: 0.0931 time to fit residues: 21.1942 Evaluate side-chains 156 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 42 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 94 optimal weight: 0.1980 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.149062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.112919 restraints weight = 45833.553| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.55 r_work: 0.2887 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13400 Z= 0.134 Angle : 0.535 7.769 18185 Z= 0.268 Chirality : 0.045 0.133 1980 Planarity : 0.003 0.030 2300 Dihedral : 13.636 133.376 1965 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.08 % Allowed : 9.32 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.22), residues: 1560 helix: 0.95 (0.23), residues: 555 sheet: -0.20 (0.24), residues: 435 loop : -1.91 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 163 TYR 0.009 0.001 TYR A 204 PHE 0.026 0.001 PHE E 228 TRP 0.015 0.001 TRP E 206 HIS 0.002 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00310 (13400) covalent geometry : angle 0.53477 (18185) hydrogen bonds : bond 0.02604 ( 575) hydrogen bonds : angle 4.46909 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2365.70 seconds wall clock time: 41 minutes 20.36 seconds (2480.36 seconds total)