Starting phenix.real_space_refine on Sat Jun 14 16:31:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgv_40469/06_2025/8sgv_40469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgv_40469/06_2025/8sgv_40469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sgv_40469/06_2025/8sgv_40469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgv_40469/06_2025/8sgv_40469.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgv_40469/06_2025/8sgv_40469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgv_40469/06_2025/8sgv_40469.cif" } resolution = 2.58 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 12 5.49 5 S 52 5.16 5 C 10415 2.51 5 N 2893 2.21 5 O 3033 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16409 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4010 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4120 Chain: "A" Number of atoms: 4010 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4120 Chain: "C" Number of atoms: 4010 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4120 Chain: "D" Number of atoms: 4015 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 499, 4011 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 462} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 499, 4011 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 462} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4125 Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLY B 121 " occ=0.82 ... (6 atoms not shown) pdb=" O BGLY B 121 " occ=0.18 residue: pdb=" N AGLY A 121 " occ=0.82 ... (6 atoms not shown) pdb=" O BGLY A 121 " occ=0.18 residue: pdb=" N AGLY C 121 " occ=0.82 ... (6 atoms not shown) pdb=" O BGLY C 121 " occ=0.18 residue: pdb=" N AGLY D 121 " occ=0.82 ... (6 atoms not shown) pdb=" O BGLY D 121 " occ=0.18 Time building chain proxies: 17.79, per 1000 atoms: 1.08 Number of scatterers: 16409 At special positions: 0 Unit cell: (113.093, 83.3755, 108.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 52 16.00 P 12 15.00 O 3033 8.00 N 2893 7.00 C 10415 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.55 Conformation dependent library (CDL) restraints added in 4.0 seconds 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3722 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 40.8% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'B' and resid 7 through 9 No H-bonds generated for 'chain 'B' and resid 7 through 9' Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 54 through 65 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 178 through 189 removed outlier: 3.562A pdb=" N VAL B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 202 through 205 removed outlier: 3.663A pdb=" N ILE B 205 " --> pdb=" O ASP B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 202 through 205' Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.618A pdb=" N HIS B 211 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET B 212 " --> pdb=" O HIS B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 212' Processing helix chain 'B' and resid 246 through 257 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 348 through 366 removed outlier: 3.681A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 471 through 486 Processing helix chain 'B' and resid 486 through 502 Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.561A pdb=" N VAL A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 202 through 205 removed outlier: 3.662A pdb=" N ILE A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.618A pdb=" N HIS A 211 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET A 212 " --> pdb=" O HIS A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.680A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 471 through 486 Processing helix chain 'A' and resid 486 through 502 Processing helix chain 'C' and resid 7 through 9 No H-bonds generated for 'chain 'C' and resid 7 through 9' Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 54 through 65 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 178 through 189 removed outlier: 3.561A pdb=" N VAL C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 202 through 205 removed outlier: 3.662A pdb=" N ILE C 205 " --> pdb=" O ASP C 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 202 through 205' Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.618A pdb=" N HIS C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET C 212 " --> pdb=" O HIS C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 212' Processing helix chain 'C' and resid 246 through 257 Processing helix chain 'C' and resid 259 through 272 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 348 through 366 removed outlier: 3.680A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 440 through 449 Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 471 through 486 Processing helix chain 'C' and resid 486 through 502 Processing helix chain 'D' and resid 7 through 9 No H-bonds generated for 'chain 'D' and resid 7 through 9' Processing helix chain 'D' and resid 10 through 19 Processing helix chain 'D' and resid 54 through 65 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 160 through 169 Processing helix chain 'D' and resid 178 through 189 removed outlier: 3.561A pdb=" N VAL D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 201 Processing helix chain 'D' and resid 202 through 205 removed outlier: 3.662A pdb=" N ILE D 205 " --> pdb=" O ASP D 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 202 through 205' Processing helix chain 'D' and resid 208 through 212 removed outlier: 3.618A pdb=" N HIS D 211 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET D 212 " --> pdb=" O HIS D 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 208 through 212' Processing helix chain 'D' and resid 246 through 257 Processing helix chain 'D' and resid 259 through 272 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 348 through 366 removed outlier: 3.680A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) Proline residue: D 359 - end of helix Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 440 through 449 Processing helix chain 'D' and resid 452 through 468 Processing helix chain 'D' and resid 471 through 486 Processing helix chain 'D' and resid 486 through 503 Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 44 removed outlier: 3.522A pdb=" N ARG D 430 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.994A pdb=" N PHE B 234 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N HIS B 218 " --> pdb=" O CYS B 232 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N CYS B 232 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE B 220 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 230 " --> pdb=" O PHE B 220 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 314 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE B 281 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE B 82 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS B 77 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 15.177A pdb=" N ASN B 142 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 14.216A pdb=" N LYS B 221 " --> pdb=" O ASN B 142 " (cutoff:3.500A) removed outlier: 13.671A pdb=" N ASP B 144 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N THR B 219 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N VAL B 146 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER B 217 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 429 through 431 removed outlier: 3.538A pdb=" N ARG B 430 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.519A pdb=" N ARG C 430 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.995A pdb=" N PHE A 234 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS A 218 " --> pdb=" O CYS A 232 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N CYS A 232 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE A 220 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 230 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 314 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE A 281 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE A 82 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS A 77 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 15.177A pdb=" N ASN A 142 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 14.215A pdb=" N LYS A 221 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 13.671A pdb=" N ASP A 144 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N THR A 219 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N VAL A 146 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER A 217 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431 removed outlier: 3.515A pdb=" N ARG A 430 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 344 removed outlier: 3.994A pdb=" N PHE C 234 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N HIS C 218 " --> pdb=" O CYS C 232 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N CYS C 232 " --> pdb=" O HIS C 218 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE C 220 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C 230 " --> pdb=" O PHE C 220 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY C 314 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE C 281 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE C 82 " --> pdb=" O ASN C 319 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS C 77 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 15.178A pdb=" N ASN C 142 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 14.216A pdb=" N LYS C 221 " --> pdb=" O ASN C 142 " (cutoff:3.500A) removed outlier: 13.671A pdb=" N ASP C 144 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N THR C 219 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N VAL C 146 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER C 217 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 343 through 344 removed outlier: 3.995A pdb=" N PHE D 234 " --> pdb=" O GLY D 216 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N HIS D 218 " --> pdb=" O CYS D 232 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N CYS D 232 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE D 220 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL D 230 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 314 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE D 281 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE D 82 " --> pdb=" O ASN D 319 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS D 77 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 15.177A pdb=" N ASN D 142 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 14.217A pdb=" N LYS D 221 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 13.672A pdb=" N ASP D 144 " --> pdb=" O THR D 219 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N THR D 219 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N VAL D 146 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N SER D 217 " --> pdb=" O VAL D 146 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1899 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 7059 1.38 - 1.55: 9745 1.55 - 1.71: 25 1.71 - 1.88: 88 1.88 - 2.04: 16 Bond restraints: 16933 Sorted by residual: bond pdb=" O2B NDP C1202 " pdb=" P2B NDP C1202 " ideal model delta sigma weight residual 1.833 1.609 0.224 3.80e-02 6.93e+02 3.49e+01 bond pdb=" O2B NDP B1202 " pdb=" P2B NDP B1202 " ideal model delta sigma weight residual 1.833 1.609 0.224 3.80e-02 6.93e+02 3.48e+01 bond pdb=" O2B NDP D1202 " pdb=" P2B NDP D1202 " ideal model delta sigma weight residual 1.833 1.609 0.224 3.80e-02 6.93e+02 3.46e+01 bond pdb=" O2B NDP A1202 " pdb=" P2B NDP A1202 " ideal model delta sigma weight residual 1.833 1.610 0.223 3.80e-02 6.93e+02 3.46e+01 bond pdb=" O5D NDP C1202 " pdb=" PN NDP C1202 " ideal model delta sigma weight residual 1.757 1.607 0.150 3.50e-02 8.16e+02 1.84e+01 ... (remaining 16928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 22821 3.24 - 6.47: 238 6.47 - 9.71: 36 9.71 - 12.95: 2 12.95 - 16.19: 10 Bond angle restraints: 23107 Sorted by residual: angle pdb=" C5B NDP A1202 " pdb=" O5B NDP A1202 " pdb=" PA NDP A1202 " ideal model delta sigma weight residual 103.84 120.03 -16.19 1.91e+00 2.73e-01 7.14e+01 angle pdb=" C5B NDP D1202 " pdb=" O5B NDP D1202 " pdb=" PA NDP D1202 " ideal model delta sigma weight residual 103.84 119.64 -15.80 1.91e+00 2.73e-01 6.81e+01 angle pdb=" C5B NDP C1202 " pdb=" O5B NDP C1202 " pdb=" PA NDP C1202 " ideal model delta sigma weight residual 103.84 119.51 -15.67 1.91e+00 2.73e-01 6.70e+01 angle pdb=" C5B NDP B1202 " pdb=" O5B NDP B1202 " pdb=" PA NDP B1202 " ideal model delta sigma weight residual 103.84 119.46 -15.62 1.91e+00 2.73e-01 6.65e+01 angle pdb=" PA NDP B1202 " pdb=" O3 NDP B1202 " pdb=" PN NDP B1202 " ideal model delta sigma weight residual 107.74 120.86 -13.12 1.95e+00 2.62e-01 4.51e+01 ... (remaining 23102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.09: 9747 25.09 - 50.18: 104 50.18 - 75.27: 28 75.27 - 100.35: 0 100.35 - 125.44: 4 Dihedral angle restraints: 9883 sinusoidal: 4080 harmonic: 5803 Sorted by residual: dihedral pdb=" C5B NDP D1202 " pdb=" O5B NDP D1202 " pdb=" PA NDP D1202 " pdb=" O3 NDP D1202 " ideal model delta sinusoidal sigma weight residual 175.04 49.60 125.44 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C5B NDP C1202 " pdb=" O5B NDP C1202 " pdb=" PA NDP C1202 " pdb=" O3 NDP C1202 " ideal model delta sinusoidal sigma weight residual 175.04 51.56 123.48 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C5B NDP B1202 " pdb=" O5B NDP B1202 " pdb=" PA NDP B1202 " pdb=" O3 NDP B1202 " ideal model delta sinusoidal sigma weight residual 175.04 51.72 123.32 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 9880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1626 0.041 - 0.083: 491 0.083 - 0.124: 187 0.124 - 0.165: 21 0.165 - 0.207: 8 Chirality restraints: 2333 Sorted by residual: chirality pdb=" C4D NDP A1202 " pdb=" C3D NDP A1202 " pdb=" C5D NDP A1202 " pdb=" O4D NDP A1202 " both_signs ideal model delta sigma weight residual False -2.71 -2.51 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C4D NDP C1202 " pdb=" C3D NDP C1202 " pdb=" C5D NDP C1202 " pdb=" O4D NDP C1202 " both_signs ideal model delta sigma weight residual False -2.71 -2.51 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C4D NDP D1202 " pdb=" C3D NDP D1202 " pdb=" C5D NDP D1202 " pdb=" O4D NDP D1202 " both_signs ideal model delta sigma weight residual False -2.71 -2.51 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2330 not shown) Planarity restraints: 3065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 346 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO B 347 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 347 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 347 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 346 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO D 347 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 347 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 347 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 346 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO A 347 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 347 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 347 " 0.026 5.00e-02 4.00e+02 ... (remaining 3062 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3867 2.79 - 3.32: 15569 3.32 - 3.84: 28803 3.84 - 4.37: 36180 4.37 - 4.90: 59816 Nonbonded interactions: 144235 Sorted by model distance: nonbonded pdb=" O ASP A 128 " pdb=" NH1 ARG A 130 " model vdw 2.260 3.120 nonbonded pdb=" O ASP B 128 " pdb=" NH1 ARG B 130 " model vdw 2.261 3.120 nonbonded pdb=" O ASP C 128 " pdb=" NH1 ARG C 130 " model vdw 2.261 3.120 nonbonded pdb=" O ASP D 128 " pdb=" NH1 ARG D 130 " model vdw 2.262 3.120 nonbonded pdb=" OD1 ASP B 360 " pdb=" NH2 ARG D 66 " model vdw 2.266 3.120 ... (remaining 144230 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 5 through 120 or resid 122 through 502 or resid 1201 throu \ gh 1202)) selection = (chain 'B' and (resid 5 through 120 or resid 122 through 502 or resid 1201 throu \ gh 1202)) selection = (chain 'C' and (resid 5 through 120 or resid 122 through 502 or resid 1201 throu \ gh 1202)) selection = (chain 'D' and (resid 5 through 120 or resid 122 through 502 or resid 1201 throu \ gh 1202)) } 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=0.18 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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 48.630 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 0.224 16937 Z= 0.239 Angle : 0.803 16.185 23107 Z= 0.385 Chirality : 0.046 0.207 2333 Planarity : 0.004 0.047 3065 Dihedral : 9.843 125.442 6161 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.23 % Allowed : 2.10 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.82 (0.19), residues: 1997 helix: 1.04 (0.19), residues: 697 sheet: 0.70 (0.31), residues: 292 loop : 0.28 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 183 HIS 0.004 0.001 HIS B 235 PHE 0.014 0.001 PHE B 136 TYR 0.018 0.002 TYR A 236 ARG 0.002 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.12937 ( 665) hydrogen bonds : angle 6.39539 ( 1899) covalent geometry : bond 0.00701 (16933) covalent geometry : angle 0.80299 (23107) Misc. bond : bond 0.01950 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 1.801 Fit side-chains outliers start: 4 outliers final: 7 residues processed: 188 average time/residue: 1.8157 time to fit residues: 370.0642 Evaluate side-chains 92 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 264 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 HIS B 352 GLN B 372 HIS A 352 GLN C 352 GLN D 352 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.076648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.063291 restraints weight = 70673.198| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.18 r_work: 0.2554 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16937 Z= 0.143 Angle : 0.571 6.107 23107 Z= 0.278 Chirality : 0.046 0.153 2333 Planarity : 0.005 0.041 3065 Dihedral : 8.810 126.827 2279 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.29 % Allowed : 6.95 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.95 (0.19), residues: 1997 helix: 1.32 (0.20), residues: 697 sheet: 0.76 (0.31), residues: 296 loop : 0.20 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 183 HIS 0.003 0.001 HIS C 194 PHE 0.015 0.002 PHE B 136 TYR 0.015 0.001 TYR A 236 ARG 0.009 0.001 ARG B 382 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 665) hydrogen bonds : angle 5.34425 ( 1899) covalent geometry : bond 0.00365 (16933) covalent geometry : angle 0.57054 (23107) Misc. bond : bond 0.02862 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 1.938 Fit side-chains REVERT: B 119 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.6977 (mt-10) REVERT: B 122 SER cc_start: 0.8489 (m) cc_final: 0.7916 (p) REVERT: B 392 MET cc_start: 0.9173 (tpp) cc_final: 0.8935 (mmm) REVERT: A 122 SER cc_start: 0.8477 (m) cc_final: 0.7907 (p) REVERT: C 119 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: C 122 SER cc_start: 0.8474 (m) cc_final: 0.7901 (p) REVERT: D 122 SER cc_start: 0.8488 (m) cc_final: 0.7921 (p) outliers start: 22 outliers final: 4 residues processed: 97 average time/residue: 1.5937 time to fit residues: 171.2409 Evaluate side-chains 77 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 132 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 79 optimal weight: 0.0270 chunk 82 optimal weight: 0.2980 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 492 HIS A 18 GLN A 492 HIS C 18 GLN C 492 HIS D 18 GLN D 492 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.080387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.066606 restraints weight = 70194.634| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.25 r_work: 0.2622 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 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 : 0.003 0.038 16937 Z= 0.106 Angle : 0.519 6.044 23107 Z= 0.249 Chirality : 0.043 0.149 2333 Planarity : 0.004 0.043 3065 Dihedral : 8.462 118.854 2273 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.23 % Allowed : 7.07 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.06 (0.19), residues: 1997 helix: 1.41 (0.20), residues: 697 sheet: 0.98 (0.31), residues: 288 loop : 0.23 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 183 HIS 0.003 0.001 HIS A 235 PHE 0.014 0.001 PHE A 136 TYR 0.014 0.001 TYR A 236 ARG 0.007 0.000 ARG C 382 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 665) hydrogen bonds : angle 5.10229 ( 1899) covalent geometry : bond 0.00268 (16933) covalent geometry : angle 0.51928 (23107) Misc. bond : bond 0.02919 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 1.851 Fit side-chains REVERT: B 122 SER cc_start: 0.8621 (m) cc_final: 0.8116 (p) REVERT: B 157 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8160 (t70) REVERT: A 122 SER cc_start: 0.8628 (m) cc_final: 0.8122 (p) REVERT: C 122 SER cc_start: 0.8622 (m) cc_final: 0.8115 (p) REVERT: C 249 ASP cc_start: 0.8540 (m-30) cc_final: 0.8302 (m-30) REVERT: D 122 SER cc_start: 0.8627 (m) cc_final: 0.8119 (p) outliers start: 21 outliers final: 4 residues processed: 92 average time/residue: 1.5945 time to fit residues: 162.1284 Evaluate side-chains 80 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 61 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN A 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.073292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.059834 restraints weight = 69091.495| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.13 r_work: 0.2505 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16937 Z= 0.217 Angle : 0.578 6.941 23107 Z= 0.288 Chirality : 0.047 0.152 2333 Planarity : 0.005 0.045 3065 Dihedral : 9.080 125.397 2273 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.17 % Allowed : 6.72 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.72 (0.18), residues: 1997 helix: 1.11 (0.19), residues: 693 sheet: 0.65 (0.30), residues: 292 loop : 0.08 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 183 HIS 0.004 0.001 HIS B 372 PHE 0.016 0.002 PHE B 136 TYR 0.017 0.002 TYR A 236 ARG 0.007 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.04826 ( 665) hydrogen bonds : angle 5.45427 ( 1899) covalent geometry : bond 0.00555 (16933) covalent geometry : angle 0.57835 (23107) Misc. bond : bond 0.05180 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 1.780 Fit side-chains REVERT: B 119 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: C 119 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7537 (mt-10) REVERT: C 249 ASP cc_start: 0.8570 (m-30) cc_final: 0.8314 (m-30) outliers start: 20 outliers final: 4 residues processed: 87 average time/residue: 1.8684 time to fit residues: 177.4470 Evaluate side-chains 72 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 58 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 55 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.2946 r_free = 0.2946 target = 0.076902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.063463 restraints weight = 64637.914| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.09 r_work: 0.2582 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16937 Z= 0.110 Angle : 0.510 6.395 23107 Z= 0.247 Chirality : 0.043 0.150 2333 Planarity : 0.004 0.043 3065 Dihedral : 8.583 118.045 2273 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.53 % Allowed : 7.77 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.18), residues: 1997 helix: 1.31 (0.20), residues: 693 sheet: 0.82 (0.31), residues: 288 loop : 0.13 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 183 HIS 0.002 0.001 HIS B 235 PHE 0.013 0.001 PHE A 136 TYR 0.015 0.001 TYR A 236 ARG 0.006 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 665) hydrogen bonds : angle 5.14919 ( 1899) covalent geometry : bond 0.00281 (16933) covalent geometry : angle 0.50973 (23107) Misc. bond : bond 0.02381 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 1.877 Fit side-chains REVERT: B 122 SER cc_start: 0.8685 (m) cc_final: 0.8108 (p) REVERT: A 122 SER cc_start: 0.8679 (m) cc_final: 0.8102 (p) REVERT: A 249 ASP cc_start: 0.8606 (m-30) cc_final: 0.8358 (m-30) REVERT: C 122 SER cc_start: 0.8667 (m) cc_final: 0.8097 (p) REVERT: C 249 ASP cc_start: 0.8597 (m-30) cc_final: 0.8350 (m-30) REVERT: D 122 SER cc_start: 0.8672 (m) cc_final: 0.8098 (p) outliers start: 9 outliers final: 4 residues processed: 91 average time/residue: 1.6990 time to fit residues: 170.2968 Evaluate side-chains 84 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 93 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.2895 r_free = 0.2895 target = 0.074206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.060642 restraints weight = 69075.729| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 3.14 r_work: 0.2504 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16937 Z= 0.184 Angle : 0.551 6.793 23107 Z= 0.272 Chirality : 0.046 0.149 2333 Planarity : 0.004 0.046 3065 Dihedral : 8.806 119.474 2273 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.93 % Allowed : 7.01 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.74 (0.18), residues: 1997 helix: 1.20 (0.20), residues: 693 sheet: 0.59 (0.30), residues: 292 loop : 0.06 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 183 HIS 0.004 0.001 HIS B 372 PHE 0.015 0.002 PHE B 136 TYR 0.017 0.001 TYR C 236 ARG 0.008 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 665) hydrogen bonds : angle 5.31275 ( 1899) covalent geometry : bond 0.00473 (16933) covalent geometry : angle 0.55128 (23107) Misc. bond : bond 0.04496 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 1.868 Fit side-chains REVERT: B 119 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: B 249 ASP cc_start: 0.8592 (m-30) cc_final: 0.8331 (m-30) REVERT: A 119 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: A 122 SER cc_start: 0.8673 (m) cc_final: 0.8087 (p) REVERT: A 249 ASP cc_start: 0.8595 (m-30) cc_final: 0.8336 (m-30) REVERT: C 119 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: C 122 SER cc_start: 0.8671 (m) cc_final: 0.8092 (p) REVERT: C 249 ASP cc_start: 0.8585 (m-30) cc_final: 0.8327 (m-30) REVERT: D 119 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: D 122 SER cc_start: 0.8677 (m) cc_final: 0.8090 (p) REVERT: D 249 ASP cc_start: 0.8594 (m-30) cc_final: 0.8336 (m-30) outliers start: 16 outliers final: 4 residues processed: 91 average time/residue: 1.8110 time to fit residues: 179.8957 Evaluate side-chains 80 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 69 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 129 optimal weight: 0.0770 chunk 107 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- 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 = 0.2889 r_free = 0.2889 target = 0.073706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.060399 restraints weight = 65092.353| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 3.05 r_work: 0.2511 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2544 r_free = 0.2544 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2544 r_free = 0.2544 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16937 Z= 0.195 Angle : 0.561 7.323 23107 Z= 0.277 Chirality : 0.046 0.149 2333 Planarity : 0.005 0.049 3065 Dihedral : 8.766 118.974 2273 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.64 % Allowed : 7.77 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.67 (0.18), residues: 1997 helix: 1.11 (0.20), residues: 693 sheet: 0.54 (0.30), residues: 292 loop : 0.05 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 183 HIS 0.004 0.001 HIS B 372 PHE 0.015 0.002 PHE A 136 TYR 0.017 0.001 TYR A 236 ARG 0.008 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 665) hydrogen bonds : angle 5.39689 ( 1899) covalent geometry : bond 0.00499 (16933) covalent geometry : angle 0.56051 (23107) Misc. bond : bond 0.04207 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.851 Fit side-chains REVERT: B 249 ASP cc_start: 0.8596 (m-30) cc_final: 0.8328 (m-30) REVERT: A 119 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7249 (mt-10) REVERT: A 122 SER cc_start: 0.8667 (m) cc_final: 0.8082 (p) REVERT: A 249 ASP cc_start: 0.8616 (m-30) cc_final: 0.8349 (m-30) REVERT: C 122 SER cc_start: 0.8692 (m) cc_final: 0.8121 (p) REVERT: C 249 ASP cc_start: 0.8599 (m-30) cc_final: 0.8334 (m-30) REVERT: D 119 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7249 (mt-10) REVERT: D 122 SER cc_start: 0.8677 (m) cc_final: 0.8093 (p) REVERT: D 249 ASP cc_start: 0.8620 (m-30) cc_final: 0.8356 (m-30) outliers start: 11 outliers final: 4 residues processed: 83 average time/residue: 1.8688 time to fit residues: 169.5626 Evaluate side-chains 78 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.0980 chunk 171 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.2939 r_free = 0.2939 target = 0.076445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.062700 restraints weight = 81861.786| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 3.38 r_work: 0.2535 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16937 Z= 0.111 Angle : 0.512 7.619 23107 Z= 0.248 Chirality : 0.043 0.149 2333 Planarity : 0.004 0.049 3065 Dihedral : 8.276 112.700 2273 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.58 % Allowed : 7.94 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.89 (0.19), residues: 1997 helix: 1.33 (0.20), residues: 693 sheet: 0.74 (0.31), residues: 288 loop : 0.13 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 183 HIS 0.002 0.001 HIS B 235 PHE 0.013 0.001 PHE A 136 TYR 0.016 0.001 TYR A 236 ARG 0.008 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 665) hydrogen bonds : angle 5.16201 ( 1899) covalent geometry : bond 0.00285 (16933) covalent geometry : angle 0.51218 (23107) Misc. bond : bond 0.02612 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 2.038 Fit side-chains REVERT: B 122 SER cc_start: 0.8673 (m) cc_final: 0.8110 (p) REVERT: B 249 ASP cc_start: 0.8595 (m-30) cc_final: 0.8342 (m-30) REVERT: A 122 SER cc_start: 0.8671 (m) cc_final: 0.8112 (p) REVERT: A 249 ASP cc_start: 0.8596 (m-30) cc_final: 0.8344 (m-30) REVERT: C 122 SER cc_start: 0.8670 (m) cc_final: 0.8110 (p) REVERT: C 249 ASP cc_start: 0.8599 (m-30) cc_final: 0.8349 (m-30) REVERT: D 122 SER cc_start: 0.8671 (m) cc_final: 0.8106 (p) REVERT: D 249 ASP cc_start: 0.8603 (m-30) cc_final: 0.8354 (m-30) outliers start: 10 outliers final: 7 residues processed: 92 average time/residue: 1.5805 time to fit residues: 161.6442 Evaluate side-chains 87 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 139 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 3 optimal weight: 0.0370 chunk 115 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 14 optimal weight: 0.0870 chunk 94 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 161 optimal weight: 0.0050 chunk 163 optimal weight: 0.8980 overall best weight: 0.3850 ------------------------------------------------------------------------------- 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 = 0.2987 r_free = 0.2987 target = 0.079436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.066124 restraints weight = 62952.180| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.05 r_work: 0.2630 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16937 Z= 0.088 Angle : 0.501 7.635 23107 Z= 0.240 Chirality : 0.042 0.148 2333 Planarity : 0.005 0.064 3065 Dihedral : 7.747 105.543 2273 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.53 % Allowed : 8.24 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.06 (0.19), residues: 1997 helix: 1.51 (0.20), residues: 693 sheet: 0.90 (0.31), residues: 288 loop : 0.18 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 183 HIS 0.002 0.000 HIS D 364 PHE 0.011 0.001 PHE D 136 TYR 0.014 0.001 TYR A 236 ARG 0.015 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 665) hydrogen bonds : angle 4.93555 ( 1899) covalent geometry : bond 0.00221 (16933) covalent geometry : angle 0.50070 (23107) Misc. bond : bond 0.02395 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 2.057 Fit side-chains REVERT: B 122 SER cc_start: 0.8676 (m) cc_final: 0.8148 (p) REVERT: B 249 ASP cc_start: 0.8611 (m-30) cc_final: 0.8371 (m-30) REVERT: A 119 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: A 122 SER cc_start: 0.8676 (m) cc_final: 0.8158 (p) REVERT: A 249 ASP cc_start: 0.8610 (m-30) cc_final: 0.8373 (m-30) REVERT: C 122 SER cc_start: 0.8663 (m) cc_final: 0.8141 (p) REVERT: C 249 ASP cc_start: 0.8613 (m-30) cc_final: 0.8376 (m-30) REVERT: D 119 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: D 122 SER cc_start: 0.8670 (m) cc_final: 0.8147 (p) REVERT: D 249 ASP cc_start: 0.8616 (m-30) cc_final: 0.8379 (m-30) outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 1.4326 time to fit residues: 162.4616 Evaluate side-chains 94 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 112 optimal weight: 0.1980 chunk 162 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN C 436 ASN D 436 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.077665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.064471 restraints weight = 62966.008| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.03 r_work: 0.2588 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16937 Z= 0.106 Angle : 0.516 9.506 23107 Z= 0.249 Chirality : 0.043 0.145 2333 Planarity : 0.005 0.057 3065 Dihedral : 7.743 104.115 2273 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.35 % Allowed : 8.64 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.03 (0.19), residues: 1997 helix: 1.40 (0.20), residues: 703 sheet: 0.86 (0.31), residues: 288 loop : 0.23 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 183 HIS 0.002 0.001 HIS B 235 PHE 0.013 0.001 PHE A 136 TYR 0.015 0.001 TYR A 236 ARG 0.014 0.001 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 665) hydrogen bonds : angle 4.96718 ( 1899) covalent geometry : bond 0.00273 (16933) covalent geometry : angle 0.51557 (23107) Misc. bond : bond 0.02864 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 1.965 Fit side-chains REVERT: B 122 SER cc_start: 0.8675 (m) cc_final: 0.8110 (p) REVERT: B 249 ASP cc_start: 0.8614 (m-30) cc_final: 0.8368 (m-30) REVERT: A 119 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: A 122 SER cc_start: 0.8673 (m) cc_final: 0.8111 (p) REVERT: A 249 ASP cc_start: 0.8611 (m-30) cc_final: 0.8367 (m-30) REVERT: C 122 SER cc_start: 0.8667 (m) cc_final: 0.8106 (p) REVERT: C 249 ASP cc_start: 0.8601 (m-30) cc_final: 0.8360 (m-30) REVERT: D 122 SER cc_start: 0.8675 (m) cc_final: 0.8113 (p) REVERT: D 249 ASP cc_start: 0.8609 (m-30) cc_final: 0.8370 (m-30) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 1.6358 time to fit residues: 162.1904 Evaluate side-chains 87 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 0.0970 chunk 168 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 177 optimal weight: 0.5980 chunk 164 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 436 ASN A 436 ASN C 436 ASN D 436 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.076071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.062690 restraints weight = 69360.247| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 3.13 r_work: 0.2552 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16937 Z= 0.136 Angle : 0.535 9.105 23107 Z= 0.260 Chirality : 0.044 0.146 2333 Planarity : 0.005 0.051 3065 Dihedral : 7.758 101.187 2273 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.29 % Allowed : 8.76 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.93 (0.19), residues: 1997 helix: 1.35 (0.20), residues: 699 sheet: 0.76 (0.30), residues: 288 loop : 0.16 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 183 HIS 0.002 0.001 HIS B 235 PHE 0.014 0.001 PHE A 136 TYR 0.016 0.001 TYR A 236 ARG 0.013 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 665) hydrogen bonds : angle 5.09241 ( 1899) covalent geometry : bond 0.00351 (16933) covalent geometry : angle 0.53480 (23107) Misc. bond : bond 0.03250 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9465.66 seconds wall clock time: 162 minutes 38.29 seconds (9758.29 seconds total)