Starting phenix.real_space_refine on Sat Jan 18 20:23:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vuw_43542/01_2025/8vuw_43542_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vuw_43542/01_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_43542/01_2025/8vuw_43542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vuw_43542/01_2025/8vuw_43542.map" model { file = "/net/cci-nas-00/data/ceres_data/8vuw_43542/01_2025/8vuw_43542_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vuw_43542/01_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-5571/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: 13.91, per 1000 atoms: 1.07 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: 3.08 Conformation dependent library (CDL) restraints added in 3.0 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: 1.41 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: 3.80 Time building geometry restraints manager: 3.62 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 38.970 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.540 ------------------------------------------------------------------------------- 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= 0.432 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 *********************** 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 : 1.472 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: 0.2464 time to fit residues: 81.3291 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 : 1.792 ------------------------------------------------------------------------------- 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 = 0.111609 restraints weight = 43319.365| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.50 r_work: 0.2874 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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= 0.284 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 *********************** 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 : 1.371 Fit side-chains REVERT: A 54 LYS cc_start: 0.8243 (mmtm) cc_final: 0.7648 (mtpt) REVERT: A 224 TRP cc_start: 0.7518 (m100) cc_final: 0.7234 (m100) REVERT: B 251 ASN cc_start: 0.8571 (m110) cc_final: 0.8223 (m110) REVERT: C 54 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7498 (mtpt) REVERT: D 148 TYR cc_start: 0.8556 (m-80) cc_final: 0.7851 (m-80) REVERT: D 265 MET cc_start: 0.8182 (ttm) cc_final: 0.7904 (ttm) REVERT: E 68 ASN cc_start: 0.8067 (m-40) cc_final: 0.7570 (m-40) REVERT: E 251 ASN cc_start: 0.8775 (m110) cc_final: 0.8415 (m-40) outliers start: 7 outliers final: 2 residues processed: 187 average time/residue: 0.2778 time to fit residues: 76.3219 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 : 1.658 ------------------------------------------------------------------------------- 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: 0.9980 chunk 67 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 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: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.152021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.120652 restraints weight = 41795.142| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.18 r_work: 0.2919 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1486 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= 0.237 Angle : 0.569 7.910 18185 Z= 0.284 Chirality : 0.045 0.148 1980 Planarity : 0.003 0.023 2300 Dihedral : 14.702 140.569 1965 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.15 % Allowed : 5.95 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1560 helix: 0.51 (0.23), residues: 555 sheet: -0.05 (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 0.002 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 *********************** 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 178 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 1.609 Fit side-chains REVERT: A 54 LYS cc_start: 0.8209 (mmtm) cc_final: 0.7716 (mtpt) REVERT: A 224 TRP cc_start: 0.7537 (m100) cc_final: 0.7314 (m100) REVERT: B 251 ASN cc_start: 0.8539 (m110) cc_final: 0.8233 (m110) REVERT: D 148 TYR cc_start: 0.8540 (m-80) cc_final: 0.7935 (m-80) REVERT: E 68 ASN cc_start: 0.8154 (m-40) cc_final: 0.7846 (m-40) REVERT: E 114 MET cc_start: 0.8941 (mtt) cc_final: 0.8481 (mtt) outliers start: 11 outliers final: 6 residues processed: 172 average time/residue: 0.2484 time to fit residues: 63.7575 Evaluate side-chains 169 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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: 0.7980 chunk 124 optimal weight: 5.9990 chunk 128 optimal weight: 0.0980 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN D 27 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.150657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.114497 restraints weight = 37638.546| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.21 r_work: 0.2931 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 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 = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13400 Z= 0.188 Angle : 0.536 7.895 18185 Z= 0.267 Chirality : 0.044 0.135 1980 Planarity : 0.003 0.021 2300 Dihedral : 14.291 139.120 1965 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.15 % Allowed : 6.88 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.69 (0.22), residues: 1560 helix: 0.72 (0.24), residues: 555 sheet: -0.07 (0.24), residues: 435 loop : -1.93 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 161 HIS 0.001 0.001 HIS B 177 PHE 0.025 0.001 PHE E 228 TYR 0.008 0.001 TYR D 204 ARG 0.003 0.000 ARG D 163 *********************** 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: 11 poor density : 165 time to evaluate : 1.426 Fit side-chains REVERT: A 54 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7540 (mtpt) REVERT: A 228 PHE cc_start: 0.7000 (t80) cc_final: 0.6716 (t80) REVERT: B 251 ASN cc_start: 0.8502 (m110) cc_final: 0.8179 (m110) REVERT: C 54 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7464 (mtpt) REVERT: D 148 TYR cc_start: 0.8418 (m-80) cc_final: 0.7901 (m-80) REVERT: E 68 ASN cc_start: 0.8119 (m-40) cc_final: 0.7774 (m-40) REVERT: E 114 MET cc_start: 0.8900 (mtt) cc_final: 0.8436 (mtt) REVERT: E 265 MET cc_start: 0.8006 (ttt) cc_final: 0.7674 (ttm) outliers start: 11 outliers final: 7 residues processed: 167 average time/residue: 0.2533 time to fit residues: 62.3676 Evaluate side-chains 168 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 104 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 14 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 59 optimal weight: 0.0770 chunk 105 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN D 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.153314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.116970 restraints weight = 44206.786| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.41 r_work: 0.2960 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13400 Z= 0.143 Angle : 0.504 7.513 18185 Z= 0.250 Chirality : 0.043 0.129 1980 Planarity : 0.003 0.020 2300 Dihedral : 13.811 136.466 1965 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.15 % Allowed : 7.60 % Favored : 91.25 % 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: -0.57 (0.22), residues: 1560 helix: 0.84 (0.24), residues: 555 sheet: -0.00 (0.24), residues: 435 loop : -1.88 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 161 HIS 0.001 0.000 HIS D 285 PHE 0.023 0.001 PHE E 228 TYR 0.007 0.001 TYR D 203 ARG 0.003 0.000 ARG B 163 *********************** 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 179 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 1.533 Fit side-chains REVERT: A 54 LYS cc_start: 0.7813 (mmtm) cc_final: 0.7544 (mtpt) REVERT: B 251 ASN cc_start: 0.8485 (m110) cc_final: 0.8214 (m110) REVERT: C 54 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7491 (mtpt) REVERT: C 148 TYR cc_start: 0.8367 (m-80) cc_final: 0.7741 (m-80) REVERT: C 155 GLU cc_start: 0.7973 (tt0) cc_final: 0.7340 (mt-10) REVERT: D 30 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6584 (tt0) REVERT: D 148 TYR cc_start: 0.8257 (m-80) cc_final: 0.7839 (m-80) REVERT: E 68 ASN cc_start: 0.8024 (m-40) cc_final: 0.7654 (m-40) REVERT: E 114 MET cc_start: 0.8903 (mtt) cc_final: 0.8428 (mtt) REVERT: E 265 MET cc_start: 0.7992 (ttt) cc_final: 0.7689 (ttm) outliers start: 11 outliers final: 6 residues processed: 172 average time/residue: 0.2398 time to fit residues: 61.4934 Evaluate side-chains 165 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET 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 30 GLU Chi-restraints excluded: chain D residue 222 VAL 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: 5.9990 chunk 106 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 182 GLN C 264 GLN E 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.146776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.110268 restraints weight = 43685.879| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.46 r_work: 0.2866 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1855 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= 0.318 Angle : 0.590 6.982 18185 Z= 0.299 Chirality : 0.046 0.147 1980 Planarity : 0.003 0.030 2300 Dihedral : 14.215 137.566 1965 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.29 % Allowed : 8.03 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.65 (0.22), residues: 1560 helix: 0.84 (0.24), residues: 555 sheet: -0.21 (0.24), residues: 435 loop : -1.87 (0.26), 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 284 PHE 0.029 0.002 PHE E 228 TYR 0.013 0.002 TYR A 204 ARG 0.004 0.000 ARG D 163 *********************** 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 163 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 1.496 Fit side-chains REVERT: B 251 ASN cc_start: 0.8570 (m110) cc_final: 0.8221 (m110) REVERT: D 49 LYS cc_start: 0.8109 (mtpt) cc_final: 0.7743 (mttt) REVERT: D 148 TYR cc_start: 0.8565 (m-80) cc_final: 0.7916 (m-80) REVERT: D 224 TRP cc_start: 0.7535 (m100) cc_final: 0.7300 (m100) REVERT: E 97 ASP cc_start: 0.8362 (p0) cc_final: 0.8090 (p0) REVERT: E 114 MET cc_start: 0.8881 (mtt) cc_final: 0.8417 (mtt) outliers start: 13 outliers final: 10 residues processed: 154 average time/residue: 0.2677 time to fit residues: 61.0864 Evaluate side-chains 157 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 1.568 ------------------------------------------------------------------------------- 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 168 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 47 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 121 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.152083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.120970 restraints weight = 45017.348| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.70 r_work: 0.2884 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13400 Z= 0.209 Angle : 0.541 7.151 18185 Z= 0.271 Chirality : 0.045 0.142 1980 Planarity : 0.003 0.025 2300 Dihedral : 13.961 136.467 1965 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.22 % Allowed : 8.67 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1560 helix: 0.89 (0.23), residues: 555 sheet: -0.21 (0.24), residues: 435 loop : -1.88 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 161 HIS 0.002 0.001 HIS A 284 PHE 0.024 0.001 PHE E 228 TYR 0.009 0.001 TYR A 204 ARG 0.003 0.000 ARG C 163 *********************** 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 171 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 1.678 Fit side-chains REVERT: A 54 LYS cc_start: 0.7883 (mmtm) cc_final: 0.7356 (mtpt) REVERT: A 97 ASP cc_start: 0.8507 (p0) cc_final: 0.8298 (p0) REVERT: B 30 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: B 251 ASN cc_start: 0.8572 (m110) cc_final: 0.8302 (m110) REVERT: D 30 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6803 (tt0) REVERT: D 148 TYR cc_start: 0.8551 (m-80) cc_final: 0.8016 (m-80) REVERT: D 224 TRP cc_start: 0.7584 (m100) cc_final: 0.7346 (m100) REVERT: E 97 ASP cc_start: 0.8363 (p0) cc_final: 0.7980 (p0) REVERT: E 114 MET cc_start: 0.8952 (mtt) cc_final: 0.8475 (mtt) outliers start: 12 outliers final: 7 residues processed: 162 average time/residue: 0.2586 time to fit residues: 62.6774 Evaluate side-chains 164 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET 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 30 GLU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 222 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 111 optimal weight: 6.9990 chunk 67 optimal weight: 0.0370 chunk 105 optimal weight: 0.0980 chunk 126 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 GLN C 182 GLN E 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.151714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.116018 restraints weight = 49387.677| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.79 r_work: 0.2921 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13400 Z= 0.150 Angle : 0.510 7.554 18185 Z= 0.255 Chirality : 0.044 0.129 1980 Planarity : 0.003 0.024 2300 Dihedral : 13.490 133.990 1965 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.15 % Allowed : 8.96 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.53 (0.22), residues: 1560 helix: 0.98 (0.24), residues: 555 sheet: -0.11 (0.24), residues: 435 loop : -1.87 (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 E 228 TYR 0.007 0.001 TYR A 203 ARG 0.003 0.000 ARG C 163 *********************** 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 182 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 1.524 Fit side-chains REVERT: A 54 LYS cc_start: 0.7825 (mmtm) cc_final: 0.7344 (mtpt) REVERT: A 97 ASP cc_start: 0.8394 (p0) cc_final: 0.8114 (p0) REVERT: A 155 GLU cc_start: 0.8129 (tt0) cc_final: 0.7476 (mt-10) REVERT: B 30 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6791 (tt0) REVERT: B 251 ASN cc_start: 0.8524 (m110) cc_final: 0.8305 (m110) REVERT: C 54 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7488 (mtpt) REVERT: C 155 GLU cc_start: 0.7960 (tt0) cc_final: 0.7333 (mt-10) REVERT: D 148 TYR cc_start: 0.8372 (m-80) cc_final: 0.7919 (m-80) REVERT: E 97 ASP cc_start: 0.8316 (p0) cc_final: 0.7937 (p0) REVERT: E 114 MET cc_start: 0.8899 (mtt) cc_final: 0.8443 (mtt) REVERT: E 265 MET cc_start: 0.8060 (ttt) cc_final: 0.7753 (ttm) outliers start: 11 outliers final: 9 residues processed: 173 average time/residue: 0.2518 time to fit residues: 64.7855 Evaluate side-chains 169 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 185 GLN 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 30 GLU Chi-restraints excluded: chain D residue 222 VAL 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: 2.9990 chunk 39 optimal weight: 3.9990 chunk 148 optimal weight: 0.1980 chunk 28 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 134 optimal weight: 0.9980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.148732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.116501 restraints weight = 48047.073| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.48 r_work: 0.2825 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13400 Z= 0.317 Angle : 0.589 7.182 18185 Z= 0.299 Chirality : 0.047 0.152 1980 Planarity : 0.003 0.032 2300 Dihedral : 13.971 135.076 1965 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.29 % Allowed : 9.10 % 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: -0.65 (0.22), residues: 1560 helix: 0.90 (0.23), residues: 555 sheet: -0.27 (0.24), residues: 435 loop : -1.88 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 161 HIS 0.003 0.001 HIS A 284 PHE 0.030 0.002 PHE E 228 TYR 0.013 0.002 TYR D 204 ARG 0.003 0.000 ARG B 163 *********************** 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 159 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.591 Fit side-chains REVERT: A 54 LYS cc_start: 0.8161 (mmtm) cc_final: 0.7663 (mtpt) REVERT: B 30 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7092 (tt0) REVERT: D 30 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.6954 (tt0) REVERT: D 49 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7722 (mttt) REVERT: D 148 TYR cc_start: 0.8629 (m-80) cc_final: 0.8024 (m-80) REVERT: D 224 TRP cc_start: 0.7654 (m100) cc_final: 0.7413 (m100) REVERT: E 97 ASP cc_start: 0.8389 (p0) cc_final: 0.7911 (p0) REVERT: E 114 MET cc_start: 0.8944 (mtt) cc_final: 0.8518 (mtt) outliers start: 13 outliers final: 9 residues processed: 149 average time/residue: 0.2512 time to fit residues: 54.8812 Evaluate side-chains 153 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 187 GLU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 30 GLU 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.4321 > 50: distance: 39 - 44: 6.092 distance: 44 - 45: 11.502 distance: 45 - 46: 15.815 distance: 45 - 48: 18.464 distance: 46 - 47: 14.948 distance: 46 - 52: 17.753 distance: 48 - 49: 25.135 distance: 49 - 50: 17.085 distance: 49 - 51: 12.971 distance: 52 - 53: 15.131 distance: 53 - 54: 23.108 distance: 53 - 56: 27.466 distance: 54 - 55: 37.131 distance: 54 - 59: 37.937 distance: 56 - 57: 28.842 distance: 56 - 58: 14.667 distance: 59 - 60: 26.522 distance: 59 - 147: 16.596 distance: 60 - 61: 25.150 distance: 60 - 63: 24.556 distance: 61 - 62: 10.617 distance: 61 - 66: 37.734 distance: 63 - 64: 20.505 distance: 63 - 65: 25.657 distance: 66 - 67: 55.824 distance: 67 - 68: 42.629 distance: 68 - 69: 50.196 distance: 68 - 70: 28.527 distance: 70 - 71: 32.959 distance: 71 - 72: 30.255 distance: 71 - 74: 8.008 distance: 72 - 73: 69.432 distance: 72 - 76: 44.263 distance: 74 - 75: 64.749 distance: 76 - 77: 45.458 distance: 76 - 82: 23.605 distance: 77 - 78: 29.386 distance: 77 - 80: 40.690 distance: 78 - 79: 50.394 distance: 78 - 83: 18.043 distance: 80 - 81: 39.072 distance: 81 - 82: 24.835 distance: 83 - 84: 9.786 distance: 84 - 85: 21.525 distance: 84 - 87: 23.274 distance: 85 - 86: 28.243 distance: 85 - 91: 36.348 distance: 87 - 88: 9.295 distance: 88 - 89: 23.725 distance: 88 - 90: 11.321 distance: 91 - 92: 17.135 distance: 92 - 93: 30.576 distance: 92 - 95: 22.881 distance: 93 - 94: 22.955 distance: 93 - 98: 28.592 distance: 95 - 96: 42.140 distance: 95 - 97: 33.035 distance: 98 - 99: 37.111 distance: 99 - 100: 12.450 distance: 100 - 101: 21.210 distance: 100 - 102: 33.009 distance: 102 - 103: 52.267 distance: 103 - 104: 40.116 distance: 103 - 106: 58.101 distance: 104 - 105: 17.161 distance: 104 - 110: 14.346 distance: 106 - 107: 68.658 distance: 107 - 108: 55.163 distance: 107 - 109: 40.220