Starting phenix.real_space_refine on Sun Aug 24 02:24:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgv_40469/08_2025/8sgv_40469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgv_40469/08_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_40469/08_2025/8sgv_40469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgv_40469/08_2025/8sgv_40469.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgv_40469/08_2025/8sgv_40469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgv_40469/08_2025/8sgv_40469.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.022 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.11, per 1000 atoms: 0.37 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: 1.04 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.46 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: 2.60 Time building geometry restraints manager: 1.40 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 1202)) selection = (chain 'B' and (resid 5 through 120 or resid 122 through 1202)) selection = (chain 'C' and (resid 5 through 120 or resid 122 through 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: 4.090 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.360 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.450 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.19), 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 ARG 0.002 0.000 ARG A 252 TYR 0.018 0.002 TYR A 236 PHE 0.014 0.001 PHE B 136 TRP 0.009 0.001 TRP A 183 HIS 0.004 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00701 (16933) covalent geometry : angle 0.80299 (23107) hydrogen bonds : bond 0.12937 ( 665) hydrogen bonds : angle 6.39539 ( 1899) 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 : 0.440 Fit side-chains outliers start: 4 outliers final: 7 residues processed: 188 average time/residue: 0.7488 time to fit residues: 152.4850 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 : 0.589 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 A 352 GLN C 352 GLN D 352 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.077073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.063944 restraints weight = 60443.684| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.98 r_work: 0.2573 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1710 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= 0.140 Angle : 0.569 6.180 23107 Z= 0.277 Chirality : 0.046 0.150 2333 Planarity : 0.005 0.040 3065 Dihedral : 8.787 125.833 2279 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.34 % Allowed : 7.13 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.19), residues: 1997 helix: 1.33 (0.20), residues: 697 sheet: 0.78 (0.31), residues: 296 loop : 0.20 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 382 TYR 0.014 0.001 TYR A 236 PHE 0.014 0.002 PHE B 136 TRP 0.013 0.001 TRP D 183 HIS 0.003 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00354 (16933) covalent geometry : angle 0.56915 (23107) hydrogen bonds : bond 0.04151 ( 665) hydrogen bonds : angle 5.32709 ( 1899) Misc. bond : bond 0.02856 ( 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 101 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.430 Fit side-chains REVERT: B 119 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.6965 (mt-10) REVERT: B 122 SER cc_start: 0.8488 (m) cc_final: 0.7936 (p) REVERT: B 392 MET cc_start: 0.9176 (tpp) cc_final: 0.8908 (mmm) REVERT: B 394 MET cc_start: 0.8539 (mpt) cc_final: 0.8290 (mpt) REVERT: A 122 SER cc_start: 0.8480 (m) cc_final: 0.7932 (p) REVERT: C 119 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.6913 (mt-10) REVERT: C 122 SER cc_start: 0.8466 (m) cc_final: 0.7916 (p) REVERT: D 122 SER cc_start: 0.8485 (m) cc_final: 0.7939 (p) outliers start: 23 outliers final: 4 residues processed: 95 average time/residue: 0.7241 time to fit residues: 75.7214 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 : 0.679 ------------------------------------------------------------------------------- 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 6 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.073611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.060369 restraints weight = 57257.088| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.91 r_work: 0.2544 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16937 Z= 0.240 Angle : 0.604 7.110 23107 Z= 0.301 Chirality : 0.049 0.153 2333 Planarity : 0.005 0.046 3065 Dihedral : 9.194 130.501 2273 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.05 % Allowed : 7.13 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.18), residues: 1997 helix: 1.01 (0.19), residues: 693 sheet: 0.58 (0.30), residues: 292 loop : 0.04 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 382 TYR 0.018 0.002 TYR A 236 PHE 0.017 0.002 PHE C 136 TRP 0.013 0.001 TRP C 183 HIS 0.005 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00613 (16933) covalent geometry : angle 0.60445 (23107) hydrogen bonds : bond 0.05096 ( 665) hydrogen bonds : angle 5.57765 ( 1899) Misc. bond : bond 0.05450 ( 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 89 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.629 Fit side-chains REVERT: C 249 ASP cc_start: 0.8554 (m-30) cc_final: 0.8292 (m-30) outliers start: 18 outliers final: 4 residues processed: 83 average time/residue: 0.8591 time to fit residues: 77.8106 Evaluate side-chains 69 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 181 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.076631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.063043 restraints weight = 72944.046| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 3.23 r_work: 0.2566 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16937 Z= 0.118 Angle : 0.522 6.812 23107 Z= 0.254 Chirality : 0.044 0.150 2333 Planarity : 0.004 0.047 3065 Dihedral : 8.726 122.182 2273 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.64 % Allowed : 7.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.18), residues: 1997 helix: 1.22 (0.20), residues: 693 sheet: 0.78 (0.31), residues: 288 loop : 0.16 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 382 TYR 0.015 0.001 TYR A 236 PHE 0.014 0.001 PHE B 136 TRP 0.012 0.001 TRP B 183 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00303 (16933) covalent geometry : angle 0.52241 (23107) hydrogen bonds : bond 0.03737 ( 665) hydrogen bonds : angle 5.23300 ( 1899) Misc. bond : bond 0.02502 ( 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: 11 poor density : 81 time to evaluate : 0.658 Fit side-chains REVERT: B 119 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7002 (mt-10) REVERT: B 122 SER cc_start: 0.8698 (m) cc_final: 0.8165 (p) REVERT: B 394 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8544 (mpt) REVERT: A 119 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7084 (mt-10) REVERT: A 122 SER cc_start: 0.8682 (m) cc_final: 0.8111 (p) REVERT: A 394 MET cc_start: 0.8817 (mmp) cc_final: 0.8261 (mpt) REVERT: C 119 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.6995 (mt-10) REVERT: C 122 SER cc_start: 0.8681 (m) cc_final: 0.8110 (p) REVERT: C 249 ASP cc_start: 0.8552 (m-30) cc_final: 0.8305 (m-30) REVERT: D 119 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: D 122 SER cc_start: 0.8686 (m) cc_final: 0.8110 (p) REVERT: D 394 MET cc_start: 0.8792 (mmp) cc_final: 0.8279 (mpt) outliers start: 11 outliers final: 4 residues processed: 89 average time/residue: 0.7515 time to fit residues: 72.8441 Evaluate side-chains 83 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 394 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 4 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 131 optimal weight: 0.0770 chunk 64 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- 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 = 0.2933 r_free = 0.2933 target = 0.076443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.062753 restraints weight = 78379.637| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.31 r_work: 0.2551 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16937 Z= 0.125 Angle : 0.516 6.595 23107 Z= 0.252 Chirality : 0.044 0.149 2333 Planarity : 0.004 0.049 3065 Dihedral : 8.687 118.554 2273 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.53 % Allowed : 7.48 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.19), residues: 1997 helix: 1.28 (0.20), residues: 693 sheet: 0.75 (0.31), residues: 288 loop : 0.17 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 382 TYR 0.015 0.001 TYR A 236 PHE 0.014 0.001 PHE B 136 TRP 0.013 0.001 TRP D 183 HIS 0.002 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00323 (16933) covalent geometry : angle 0.51626 (23107) hydrogen bonds : bond 0.03841 ( 665) hydrogen bonds : angle 5.19162 ( 1899) Misc. bond : bond 0.03219 ( 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 96 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.643 Fit side-chains REVERT: B 119 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7002 (mt-10) REVERT: B 122 SER cc_start: 0.8693 (m) cc_final: 0.8093 (p) REVERT: B 249 ASP cc_start: 0.8600 (m-30) cc_final: 0.8350 (m-30) REVERT: A 122 SER cc_start: 0.8669 (m) cc_final: 0.8090 (p) REVERT: A 249 ASP cc_start: 0.8602 (m-30) cc_final: 0.8353 (m-30) REVERT: A 394 MET cc_start: 0.8781 (mmp) cc_final: 0.8254 (mpt) REVERT: C 119 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7020 (mt-10) REVERT: C 122 SER cc_start: 0.8667 (m) cc_final: 0.8084 (p) REVERT: C 249 ASP cc_start: 0.8602 (m-30) cc_final: 0.8353 (m-30) REVERT: D 119 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: D 122 SER cc_start: 0.8665 (m) cc_final: 0.8078 (p) REVERT: D 249 ASP cc_start: 0.8603 (m-30) cc_final: 0.8356 (m-30) REVERT: D 394 MET cc_start: 0.8834 (mmp) cc_final: 0.8332 (mpt) outliers start: 9 outliers final: 4 residues processed: 95 average time/residue: 0.7786 time to fit residues: 80.6843 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 : 0.602 ------------------------------------------------------------------------------- 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 119 GLU 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 174 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 176 optimal weight: 0.0470 chunk 5 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- 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 = 0.2914 r_free = 0.2914 target = 0.075160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.061392 restraints weight = 85021.864| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 3.43 r_work: 0.2531 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2490 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= 0.140 Angle : 0.522 6.617 23107 Z= 0.256 Chirality : 0.044 0.149 2333 Planarity : 0.005 0.049 3065 Dihedral : 8.620 116.776 2273 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.64 % Allowed : 7.13 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.18), residues: 1997 helix: 1.28 (0.20), residues: 693 sheet: 0.64 (0.30), residues: 292 loop : 0.13 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 382 TYR 0.016 0.001 TYR A 236 PHE 0.014 0.001 PHE B 136 TRP 0.013 0.001 TRP D 183 HIS 0.003 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00359 (16933) covalent geometry : angle 0.52183 (23107) hydrogen bonds : bond 0.03989 ( 665) hydrogen bonds : angle 5.21575 ( 1899) Misc. bond : bond 0.03416 ( 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 90 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.523 Fit side-chains REVERT: B 119 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7020 (mt-10) REVERT: B 122 SER cc_start: 0.8684 (m) cc_final: 0.8112 (p) REVERT: B 138 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8691 (p) REVERT: A 122 SER cc_start: 0.8657 (m) cc_final: 0.8084 (p) REVERT: A 138 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8691 (p) REVERT: A 249 ASP cc_start: 0.8603 (m-30) cc_final: 0.8351 (m-30) REVERT: C 119 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: C 122 SER cc_start: 0.8661 (m) cc_final: 0.8084 (p) REVERT: C 138 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8689 (p) REVERT: C 249 ASP cc_start: 0.8605 (m-30) cc_final: 0.8353 (m-30) REVERT: D 119 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7114 (mt-10) REVERT: D 122 SER cc_start: 0.8664 (m) cc_final: 0.8089 (p) outliers start: 11 outliers final: 4 residues processed: 90 average time/residue: 0.8008 time to fit residues: 78.8335 Evaluate side-chains 89 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 138 THR 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 95 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 9 optimal weight: 0.0010 chunk 188 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 overall best weight: 0.8992 ------------------------------------------------------------------------------- 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 = 0.2937 r_free = 0.2937 target = 0.076419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.062968 restraints weight = 70463.184| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.17 r_work: 0.2563 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16937 Z= 0.118 Angle : 0.513 8.020 23107 Z= 0.249 Chirality : 0.043 0.149 2333 Planarity : 0.004 0.049 3065 Dihedral : 8.431 113.911 2273 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.76 % Allowed : 7.30 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.19), residues: 1997 helix: 1.34 (0.20), residues: 693 sheet: 0.72 (0.30), residues: 288 loop : 0.18 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.015 0.001 TYR A 236 PHE 0.013 0.001 PHE D 136 TRP 0.012 0.001 TRP A 183 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00305 (16933) covalent geometry : angle 0.51272 (23107) hydrogen bonds : bond 0.03715 ( 665) hydrogen bonds : angle 5.13457 ( 1899) Misc. bond : bond 0.02743 ( 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 100 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.588 Fit side-chains REVERT: B 119 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.6990 (mt-10) REVERT: B 122 SER cc_start: 0.8684 (m) cc_final: 0.8105 (p) REVERT: B 138 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8726 (p) REVERT: A 122 SER cc_start: 0.8676 (m) cc_final: 0.8104 (p) REVERT: A 138 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8719 (p) REVERT: A 249 ASP cc_start: 0.8593 (m-30) cc_final: 0.8342 (m-30) REVERT: C 119 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7072 (mt-10) REVERT: C 122 SER cc_start: 0.8677 (m) cc_final: 0.8097 (p) REVERT: C 138 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8721 (p) REVERT: C 249 ASP cc_start: 0.8593 (m-30) cc_final: 0.8345 (m-30) REVERT: D 119 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7074 (mt-10) REVERT: D 122 SER cc_start: 0.8676 (m) cc_final: 0.8095 (p) REVERT: D 138 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8723 (p) REVERT: D 249 ASP cc_start: 0.8592 (m-30) cc_final: 0.8341 (m-30) outliers start: 13 outliers final: 4 residues processed: 100 average time/residue: 0.6874 time to fit residues: 75.4008 Evaluate side-chains 95 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 138 THR 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 44 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 128 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 165 optimal weight: 0.5980 chunk 57 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.2985 r_free = 0.2985 target = 0.079122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.065622 restraints weight = 72982.564| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.25 r_work: 0.2601 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16937 Z= 0.092 Angle : 0.498 8.761 23107 Z= 0.239 Chirality : 0.042 0.147 2333 Planarity : 0.004 0.057 3065 Dihedral : 8.038 108.361 2273 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.76 % Allowed : 7.42 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.19), residues: 1997 helix: 1.48 (0.20), residues: 693 sheet: 0.87 (0.30), residues: 288 loop : 0.20 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 19 TYR 0.014 0.001 TYR C 236 PHE 0.012 0.001 PHE C 136 TRP 0.011 0.001 TRP A 183 HIS 0.002 0.000 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00234 (16933) covalent geometry : angle 0.49800 (23107) hydrogen bonds : bond 0.03221 ( 665) hydrogen bonds : angle 4.95438 ( 1899) Misc. bond : bond 0.02360 ( 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 115 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.682 Fit side-chains REVERT: B 119 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.6945 (mt-10) REVERT: B 122 SER cc_start: 0.8685 (m) cc_final: 0.8139 (p) REVERT: B 138 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8805 (p) REVERT: B 249 ASP cc_start: 0.8584 (m-30) cc_final: 0.8346 (m-30) REVERT: A 119 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: A 122 SER cc_start: 0.8684 (m) cc_final: 0.8128 (p) REVERT: A 138 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8800 (p) REVERT: A 249 ASP cc_start: 0.8585 (m-30) cc_final: 0.8349 (m-30) REVERT: C 122 SER cc_start: 0.8673 (m) cc_final: 0.8118 (p) REVERT: C 138 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8804 (p) REVERT: C 249 ASP cc_start: 0.8583 (m-30) cc_final: 0.8349 (m-30) REVERT: D 122 SER cc_start: 0.8684 (m) cc_final: 0.8126 (p) REVERT: D 138 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8797 (p) REVERT: D 249 ASP cc_start: 0.8592 (m-30) cc_final: 0.8355 (m-30) REVERT: D 394 MET cc_start: 0.8773 (mpp) cc_final: 0.8530 (mmp) outliers start: 13 outliers final: 5 residues processed: 109 average time/residue: 0.6425 time to fit residues: 77.5410 Evaluate side-chains 102 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 138 THR 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 128 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 436 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.074872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.061454 restraints weight = 68399.297| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 3.10 r_work: 0.2514 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16937 Z= 0.165 Angle : 0.543 11.074 23107 Z= 0.265 Chirality : 0.045 0.147 2333 Planarity : 0.004 0.049 3065 Dihedral : 8.349 112.472 2273 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.64 % Allowed : 7.54 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.19), residues: 1997 helix: 1.29 (0.20), residues: 693 sheet: 0.60 (0.30), residues: 292 loop : 0.13 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 19 TYR 0.016 0.001 TYR A 236 PHE 0.014 0.002 PHE C 136 TRP 0.013 0.001 TRP A 183 HIS 0.003 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00425 (16933) covalent geometry : angle 0.54253 (23107) hydrogen bonds : bond 0.04192 ( 665) hydrogen bonds : angle 5.22296 ( 1899) Misc. bond : bond 0.04275 ( 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 93 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.542 Fit side-chains REVERT: B 119 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.6943 (mt-10) REVERT: B 122 SER cc_start: 0.8654 (m) cc_final: 0.8050 (p) REVERT: B 138 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8672 (p) REVERT: B 249 ASP cc_start: 0.8566 (m-30) cc_final: 0.8310 (m-30) REVERT: A 122 SER cc_start: 0.8653 (m) cc_final: 0.8069 (p) REVERT: A 138 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8682 (p) REVERT: A 249 ASP cc_start: 0.8559 (m-30) cc_final: 0.8302 (m-30) REVERT: C 122 SER cc_start: 0.8642 (m) cc_final: 0.8056 (p) REVERT: C 138 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8682 (p) REVERT: C 249 ASP cc_start: 0.8576 (m-30) cc_final: 0.8321 (m-30) REVERT: D 119 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7090 (mt-10) REVERT: D 122 SER cc_start: 0.8651 (m) cc_final: 0.8066 (p) REVERT: D 138 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8679 (p) REVERT: D 249 ASP cc_start: 0.8571 (m-30) cc_final: 0.8314 (m-30) outliers start: 11 outliers final: 4 residues processed: 93 average time/residue: 0.8197 time to fit residues: 83.3344 Evaluate side-chains 91 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 138 THR 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 162 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 179 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.2957 r_free = 0.2957 target = 0.077573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.064216 restraints weight = 67329.173| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.12 r_work: 0.2583 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2560 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= 0.103 Angle : 0.523 11.669 23107 Z= 0.250 Chirality : 0.042 0.149 2333 Planarity : 0.005 0.053 3065 Dihedral : 7.925 109.019 2273 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.64 % Allowed : 8.06 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.19), residues: 1997 helix: 1.42 (0.20), residues: 689 sheet: 0.82 (0.30), residues: 288 loop : 0.18 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 19 TYR 0.014 0.001 TYR A 236 PHE 0.012 0.001 PHE C 136 TRP 0.011 0.001 TRP A 183 HIS 0.002 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00261 (16933) covalent geometry : angle 0.52330 (23107) hydrogen bonds : bond 0.03475 ( 665) hydrogen bonds : angle 5.08061 ( 1899) Misc. bond : bond 0.02404 ( 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 100 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.696 Fit side-chains REVERT: B 119 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.6961 (mt-10) REVERT: B 122 SER cc_start: 0.8681 (m) cc_final: 0.8105 (p) REVERT: B 138 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8767 (p) REVERT: B 249 ASP cc_start: 0.8587 (m-30) cc_final: 0.8337 (m-30) REVERT: A 122 SER cc_start: 0.8688 (m) cc_final: 0.8130 (p) REVERT: A 138 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8753 (p) REVERT: A 249 ASP cc_start: 0.8586 (m-30) cc_final: 0.8336 (m-30) REVERT: C 122 SER cc_start: 0.8667 (m) cc_final: 0.8098 (p) REVERT: C 138 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8757 (p) REVERT: C 249 ASP cc_start: 0.8597 (m-30) cc_final: 0.8349 (m-30) REVERT: C 394 MET cc_start: 0.8720 (mpp) cc_final: 0.8317 (mmp) REVERT: D 122 SER cc_start: 0.8681 (m) cc_final: 0.8123 (p) REVERT: D 138 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8769 (p) REVERT: D 249 ASP cc_start: 0.8596 (m-30) cc_final: 0.8347 (m-30) outliers start: 11 outliers final: 4 residues processed: 99 average time/residue: 0.7698 time to fit residues: 84.1018 Evaluate side-chains 93 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 138 THR 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 73 optimal weight: 4.9990 chunk 85 optimal weight: 0.0010 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 183 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- 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 = 0.077000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.063790 restraints weight = 59454.283| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.99 r_work: 0.2583 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16937 Z= 0.119 Angle : 0.539 11.327 23107 Z= 0.260 Chirality : 0.043 0.147 2333 Planarity : 0.004 0.050 3065 Dihedral : 7.896 108.221 2273 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.58 % Allowed : 8.06 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.18), residues: 1997 helix: 1.17 (0.20), residues: 717 sheet: 0.77 (0.30), residues: 288 loop : 0.17 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 19 TYR 0.015 0.001 TYR A 236 PHE 0.013 0.001 PHE A 136 TRP 0.012 0.001 TRP A 183 HIS 0.002 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00307 (16933) covalent geometry : angle 0.53854 (23107) hydrogen bonds : bond 0.03622 ( 665) hydrogen bonds : angle 5.06304 ( 1899) Misc. bond : bond 0.02945 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4370.29 seconds wall clock time: 75 minutes 32.85 seconds (4532.85 seconds total)