Starting phenix.real_space_refine on Wed Jul 30 21:19:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vuw_43542/07_2025/8vuw_43542_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vuw_43542/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vuw_43542/07_2025/8vuw_43542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vuw_43542/07_2025/8vuw_43542.map" model { file = "/net/cci-nas-00/data/ceres_data/8vuw_43542/07_2025/8vuw_43542_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vuw_43542/07_2025/8vuw_43542_neut.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 14.09, per 1000 atoms: 1.08 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: 3.42 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 2.95 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: 5.67 Time building geometry restraints manager: 3.92 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: 0.290 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 43.410 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.120 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:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.620 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.002 TRP D 161 HIS 0.004 0.002 HIS C 177 PHE 0.017 0.003 PHE D 223 TYR 0.015 0.002 TYR E 245 ARG 0.002 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.12095 ( 575) hydrogen bonds : angle 6.19211 ( 1800) covalent geometry : bond 0.00680 (13400) covalent geometry : angle 0.97882 (18185) *********************** 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 : 1.339 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: 0.2613 time to fit residues: 86.6052 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 : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 0.0270 chunk 62 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 overall best weight: 1.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 233 GLN B B 68 ASN B 233 GLN B C 68 ASN C 233 GLN B C 251 ASN D 68 ASN D 233 GLN B E 68 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.148423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.111610 restraints weight = 43319.366| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.50 r_work: 0.2875 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13400 Z= 0.189 Angle : 0.615 6.750 18185 Z= 0.307 Chirality : 0.046 0.149 1980 Planarity : 0.004 0.033 2300 Dihedral : 15.720 141.942 1965 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.86 % Allowed : 4.30 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1560 helix: -0.17 (0.22), residues: 585 sheet: -0.08 (0.23), residues: 470 loop : -2.07 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 161 HIS 0.002 0.001 HIS C 177 PHE 0.013 0.002 PHE B 121 TYR 0.011 0.002 TYR D 204 ARG 0.005 0.000 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 575) hydrogen bonds : angle 4.84312 ( 1800) covalent geometry : bond 0.00441 (13400) covalent geometry : angle 0.61482 (18185) *********************** 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 189 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 1.499 Fit side-chains REVERT: A 54 LYS cc_start: 0.8237 (mmtm) cc_final: 0.7643 (mtpt) REVERT: A 224 TRP cc_start: 0.7516 (m100) cc_final: 0.7232 (m100) REVERT: B 251 ASN cc_start: 0.8571 (m110) cc_final: 0.8221 (m110) REVERT: C 54 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7492 (mtpt) REVERT: D 148 TYR cc_start: 0.8553 (m-80) cc_final: 0.7848 (m-80) REVERT: D 265 MET cc_start: 0.8177 (ttm) cc_final: 0.7896 (ttm) REVERT: E 68 ASN cc_start: 0.8064 (m-40) cc_final: 0.7567 (m-40) REVERT: E 251 ASN cc_start: 0.8774 (m110) cc_final: 0.8412 (m-40) outliers start: 7 outliers final: 2 residues processed: 187 average time/residue: 0.2719 time to fit residues: 75.3176 Evaluate side-chains 163 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 1.618 ------------------------------------------------------------------------------- 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 72 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 89 ASN D 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.153446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.123055 restraints weight = 41642.577| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.99 r_work: 0.2918 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.096 | | 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: 0.7920 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13400 Z= 0.157 Angle : 0.568 8.162 18185 Z= 0.283 Chirality : 0.045 0.145 1980 Planarity : 0.003 0.024 2300 Dihedral : 14.613 140.354 1965 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.15 % Allowed : 5.81 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.22), residues: 1560 helix: 0.52 (0.23), residues: 555 sheet: -0.04 (0.24), residues: 435 loop : -1.93 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 161 HIS 0.001 0.001 HIS C 177 PHE 0.013 0.001 PHE B 228 TYR 0.010 0.001 TYR A 204 ARG 0.005 0.000 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.02870 ( 575) hydrogen bonds : angle 4.63910 ( 1800) covalent geometry : bond 0.00365 (13400) covalent geometry : angle 0.56817 (18185) *********************** 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: 11 poor density : 168 time to evaluate : 1.638 Fit side-chains REVERT: A 54 LYS cc_start: 0.8179 (mmtm) cc_final: 0.7688 (mtpt) REVERT: A 224 TRP cc_start: 0.7501 (m100) cc_final: 0.7287 (m100) REVERT: B 251 ASN cc_start: 0.8531 (m110) cc_final: 0.8208 (m110) REVERT: D 148 TYR cc_start: 0.8523 (m-80) cc_final: 0.7923 (m-80) REVERT: E 68 ASN cc_start: 0.8128 (m-40) cc_final: 0.7817 (m-40) REVERT: E 114 MET cc_start: 0.8918 (mtt) cc_final: 0.8437 (mtt) outliers start: 11 outliers final: 6 residues processed: 173 average time/residue: 0.3925 time to fit residues: 99.9085 Evaluate side-chains 163 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 2.171 ------------------------------------------------------------------------------- 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 113 ASP 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 114 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 128 optimal weight: 0.0030 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 67 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN C 89 ASN D 27 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.157123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.129352 restraints weight = 37351.763| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.39 r_work: 0.2985 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 13400 Z= 0.109 Angle : 0.522 8.118 18185 Z= 0.259 Chirality : 0.044 0.131 1980 Planarity : 0.003 0.020 2300 Dihedral : 14.179 138.474 1965 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.93 % Allowed : 6.81 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.22), residues: 1560 helix: 0.72 (0.24), residues: 555 sheet: -0.04 (0.24), residues: 435 loop : -1.93 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 161 HIS 0.001 0.000 HIS D 177 PHE 0.025 0.001 PHE A 228 TYR 0.007 0.001 TYR D 203 ARG 0.003 0.000 ARG B 286 Details of bonding type rmsd hydrogen bonds : bond 0.02462 ( 575) hydrogen bonds : angle 4.43855 ( 1800) covalent geometry : bond 0.00244 (13400) covalent geometry : angle 0.52179 (18185) *********************** 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 176 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 3.741 Fit side-chains REVERT: A 54 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7554 (mtpt) REVERT: A 224 TRP cc_start: 0.7409 (m100) cc_final: 0.7197 (m100) REVERT: B 251 ASN cc_start: 0.8479 (m110) cc_final: 0.8207 (m110) REVERT: C 54 LYS cc_start: 0.8074 (mmtm) cc_final: 0.7487 (mtpt) REVERT: D 148 TYR cc_start: 0.8324 (m-80) cc_final: 0.7852 (m-80) REVERT: E 68 ASN cc_start: 0.8101 (m-40) cc_final: 0.7754 (m-40) REVERT: E 114 MET cc_start: 0.8895 (mtt) cc_final: 0.8418 (mtt) REVERT: E 251 ASN cc_start: 0.8656 (m110) cc_final: 0.8258 (m-40) REVERT: E 265 MET cc_start: 0.8007 (ttt) cc_final: 0.7680 (ttm) outliers start: 8 outliers final: 5 residues processed: 170 average time/residue: 0.4299 time to fit residues: 108.8620 Evaluate side-chains 164 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 159 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET 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 104 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 4 optimal weight: 0.0270 chunk 14 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN C 264 GLN E 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.146234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.109548 restraints weight = 44317.842| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.46 r_work: 0.2860 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13400 Z= 0.209 Angle : 0.593 6.956 18185 Z= 0.300 Chirality : 0.046 0.151 1980 Planarity : 0.003 0.028 2300 Dihedral : 14.491 139.421 1965 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.29 % Allowed : 7.24 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.22), residues: 1560 helix: 0.73 (0.24), residues: 555 sheet: -0.22 (0.24), residues: 435 loop : -1.93 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 161 HIS 0.002 0.001 HIS A 284 PHE 0.029 0.002 PHE A 228 TYR 0.014 0.002 TYR A 204 ARG 0.004 0.000 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 575) hydrogen bonds : angle 4.67919 ( 1800) covalent geometry : bond 0.00495 (13400) covalent geometry : angle 0.59344 (18185) *********************** 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 169 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 2.018 Fit side-chains REVERT: B 251 ASN cc_start: 0.8584 (m110) cc_final: 0.8228 (m110) REVERT: D 148 TYR cc_start: 0.8587 (m-80) cc_final: 0.7930 (m-80) REVERT: D 224 TRP cc_start: 0.7527 (m100) cc_final: 0.7275 (m100) REVERT: E 114 MET cc_start: 0.8871 (mtt) cc_final: 0.8420 (mtt) outliers start: 13 outliers final: 8 residues processed: 161 average time/residue: 0.2518 time to fit residues: 61.0046 Evaluate side-chains 158 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 113 ASP 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 44 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 102 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 chunk 113 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 70 optimal weight: 0.1980 chunk 3 optimal weight: 6.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN D 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.152431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.116500 restraints weight = 43657.519| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.30 r_work: 0.2953 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 13400 Z= 0.101 Angle : 0.512 8.011 18185 Z= 0.253 Chirality : 0.044 0.129 1980 Planarity : 0.003 0.020 2300 Dihedral : 13.870 136.439 1965 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.22 % Allowed : 7.74 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1560 helix: 0.81 (0.23), residues: 555 sheet: -0.12 (0.24), residues: 435 loop : -1.93 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 161 HIS 0.002 0.001 HIS B 285 PHE 0.023 0.001 PHE A 228 TYR 0.006 0.001 TYR A 203 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02378 ( 575) hydrogen bonds : angle 4.40062 ( 1800) covalent geometry : bond 0.00223 (13400) covalent geometry : angle 0.51161 (18185) *********************** 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 175 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 1.517 Fit side-chains REVERT: A 54 LYS cc_start: 0.7839 (mmtm) cc_final: 0.7243 (mtpt) REVERT: B 30 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6690 (tt0) REVERT: C 54 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7497 (mtpt) REVERT: C 155 GLU cc_start: 0.8052 (tt0) cc_final: 0.7435 (mt-10) REVERT: D 148 TYR cc_start: 0.8309 (m-80) cc_final: 0.7854 (m-80) REVERT: D 224 TRP cc_start: 0.7530 (m100) cc_final: 0.7295 (m100) REVERT: E 97 ASP cc_start: 0.8316 (p0) cc_final: 0.7952 (p0) REVERT: E 114 MET cc_start: 0.8909 (mtt) cc_final: 0.8434 (mtt) REVERT: E 265 MET cc_start: 0.7998 (ttt) cc_final: 0.7693 (ttm) outliers start: 12 outliers final: 7 residues processed: 167 average time/residue: 0.2557 time to fit residues: 64.7011 Evaluate side-chains 160 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET 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 47 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 35 optimal weight: 0.0670 chunk 17 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.3627 r_free = 0.3627 target = 0.154085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.121990 restraints weight = 44889.101| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.28 r_work: 0.2938 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13400 Z= 0.116 Angle : 0.516 7.373 18185 Z= 0.258 Chirality : 0.044 0.130 1980 Planarity : 0.003 0.023 2300 Dihedral : 13.672 134.796 1965 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.00 % Allowed : 8.60 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1560 helix: 0.93 (0.24), residues: 555 sheet: -0.05 (0.24), residues: 435 loop : -1.83 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 161 HIS 0.002 0.001 HIS B 285 PHE 0.024 0.001 PHE A 228 TYR 0.007 0.001 TYR C 203 ARG 0.002 0.000 ARG C 163 Details of bonding type rmsd hydrogen bonds : bond 0.02455 ( 575) hydrogen bonds : angle 4.35105 ( 1800) covalent geometry : bond 0.00264 (13400) covalent geometry : angle 0.51585 (18185) *********************** 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: 9 poor density : 161 time to evaluate : 1.406 Fit side-chains REVERT: A 54 LYS cc_start: 0.7827 (mmtm) cc_final: 0.7370 (mtpt) REVERT: A 97 ASP cc_start: 0.8418 (p0) cc_final: 0.8146 (p0) REVERT: B 30 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6869 (tt0) REVERT: C 54 LYS cc_start: 0.8121 (mmtm) cc_final: 0.7456 (mtpt) REVERT: C 155 GLU cc_start: 0.8067 (tt0) cc_final: 0.7468 (mt-10) REVERT: D 224 TRP cc_start: 0.7565 (m100) cc_final: 0.7326 (m100) REVERT: E 97 ASP cc_start: 0.8323 (p0) cc_final: 0.7961 (p0) REVERT: E 114 MET cc_start: 0.8912 (mtt) cc_final: 0.8441 (mtt) REVERT: E 265 MET cc_start: 0.8071 (ttt) cc_final: 0.7760 (ttm) outliers start: 9 outliers final: 7 residues processed: 162 average time/residue: 0.2389 time to fit residues: 58.0673 Evaluate side-chains 167 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.149798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.117378 restraints weight = 49418.991| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.57 r_work: 0.2840 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13400 Z= 0.191 Angle : 0.575 7.320 18185 Z= 0.291 Chirality : 0.046 0.146 1980 Planarity : 0.003 0.028 2300 Dihedral : 13.983 135.544 1965 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.15 % Allowed : 9.03 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.22), residues: 1560 helix: 0.89 (0.23), residues: 555 sheet: -0.22 (0.24), residues: 435 loop : -1.85 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 161 HIS 0.002 0.001 HIS B 284 PHE 0.030 0.002 PHE A 228 TYR 0.012 0.002 TYR D 204 ARG 0.003 0.000 ARG C 163 Details of bonding type rmsd hydrogen bonds : bond 0.02960 ( 575) hydrogen bonds : angle 4.59718 ( 1800) covalent geometry : bond 0.00452 (13400) covalent geometry : angle 0.57511 (18185) *********************** 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 166 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 1.331 Fit side-chains REVERT: A 54 LYS cc_start: 0.7946 (mmtm) cc_final: 0.7406 (mtpt) REVERT: A 97 ASP cc_start: 0.8527 (p0) cc_final: 0.8268 (p0) REVERT: B 30 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7090 (tt0) REVERT: D 49 LYS cc_start: 0.8103 (mtpt) cc_final: 0.7726 (mttt) REVERT: D 148 TYR cc_start: 0.8599 (m-80) cc_final: 0.8016 (m-80) REVERT: D 224 TRP cc_start: 0.7656 (m100) cc_final: 0.7421 (m100) REVERT: E 114 MET cc_start: 0.8951 (mtt) cc_final: 0.8500 (mtt) outliers start: 11 outliers final: 8 residues processed: 157 average time/residue: 0.2577 time to fit residues: 60.5649 Evaluate side-chains 156 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 153 optimal weight: 0.3980 chunk 127 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.150475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.113976 restraints weight = 48164.243| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.59 r_work: 0.2891 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2082 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= 0.118 Angle : 0.519 7.404 18185 Z= 0.259 Chirality : 0.044 0.133 1980 Planarity : 0.003 0.023 2300 Dihedral : 13.526 133.833 1965 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.00 % Allowed : 9.32 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.22), residues: 1560 helix: 0.95 (0.23), residues: 555 sheet: -0.14 (0.24), residues: 435 loop : -1.86 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 161 HIS 0.002 0.001 HIS B 284 PHE 0.022 0.001 PHE E 228 TYR 0.007 0.001 TYR A 204 ARG 0.005 0.000 ARG C 163 Details of bonding type rmsd hydrogen bonds : bond 0.02463 ( 575) hydrogen bonds : angle 4.41809 ( 1800) covalent geometry : bond 0.00268 (13400) covalent geometry : angle 0.51890 (18185) *********************** 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 160 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 1.441 Fit side-chains REVERT: A 54 LYS cc_start: 0.7863 (mmtm) cc_final: 0.7360 (mtpt) REVERT: B 30 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6803 (tt0) REVERT: C 54 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7458 (mtpt) REVERT: C 155 GLU cc_start: 0.7937 (tt0) cc_final: 0.7241 (mt-10) REVERT: D 148 TYR cc_start: 0.8453 (m-80) cc_final: 0.7986 (m-80) REVERT: D 224 TRP cc_start: 0.7571 (m100) cc_final: 0.7351 (m100) REVERT: E 97 ASP cc_start: 0.8323 (p0) cc_final: 0.7973 (p0) REVERT: E 114 MET cc_start: 0.8927 (mtt) cc_final: 0.8446 (mtt) REVERT: E 265 MET cc_start: 0.8061 (ttt) cc_final: 0.7759 (ttm) outliers start: 9 outliers final: 7 residues processed: 153 average time/residue: 0.2446 time to fit residues: 56.3419 Evaluate side-chains 160 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.145564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.108823 restraints weight = 41065.060| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.27 r_work: 0.2846 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13400 Z= 0.229 Angle : 0.606 6.859 18185 Z= 0.308 Chirality : 0.047 0.152 1980 Planarity : 0.004 0.038 2300 Dihedral : 14.054 134.981 1965 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1560 helix: 0.84 (0.23), residues: 555 sheet: -0.30 (0.24), residues: 435 loop : -1.90 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 161 HIS 0.003 0.001 HIS C 284 PHE 0.031 0.002 PHE E 228 TYR 0.014 0.002 TYR D 204 ARG 0.003 0.000 ARG C 163 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 575) hydrogen bonds : angle 4.68993 ( 1800) covalent geometry : bond 0.00543 (13400) covalent geometry : angle 0.60627 (18185) ********************** 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 161 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 1.287 Fit side-chains REVERT: A 54 LYS cc_start: 0.8151 (mmtm) cc_final: 0.7618 (mtpt) REVERT: B 30 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7075 (tt0) REVERT: D 148 TYR cc_start: 0.8637 (m-80) cc_final: 0.8016 (m-80) REVERT: D 224 TRP cc_start: 0.7657 (m100) cc_final: 0.7421 (m100) REVERT: E 114 MET cc_start: 0.8932 (mtt) cc_final: 0.8497 (mtt) outliers start: 10 outliers final: 7 residues processed: 155 average time/residue: 0.2434 time to fit residues: 56.2269 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 : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 145 optimal weight: 0.0060 chunk 41 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.149652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.113398 restraints weight = 48612.166| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.46 r_work: 0.2885 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2125 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= 0.121 Angle : 0.528 7.478 18185 Z= 0.264 Chirality : 0.044 0.134 1980 Planarity : 0.003 0.025 2300 Dihedral : 13.575 133.223 1965 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.93 % Allowed : 9.53 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.22), residues: 1560 helix: 0.93 (0.23), residues: 555 sheet: -0.23 (0.24), residues: 435 loop : -1.89 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 161 HIS 0.002 0.001 HIS B 285 PHE 0.023 0.001 PHE E 228 TYR 0.008 0.001 TYR C 203 ARG 0.005 0.000 ARG C 163 Details of bonding type rmsd hydrogen bonds : bond 0.02541 ( 575) hydrogen bonds : angle 4.49183 ( 1800) covalent geometry : bond 0.00271 (13400) covalent geometry : angle 0.52768 (18185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6869.10 seconds wall clock time: 125 minutes 29.20 seconds (7529.20 seconds total)