Starting phenix.real_space_refine on Thu Mar 5 23:48:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6si8_10208/03_2026/6si8_10208_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6si8_10208/03_2026/6si8_10208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6si8_10208/03_2026/6si8_10208_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6si8_10208/03_2026/6si8_10208_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6si8_10208/03_2026/6si8_10208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6si8_10208/03_2026/6si8_10208.map" } resolution = 3.4 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= 0.001 sd= 0.091 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 P 4 5.49 5 S 86 5.16 5 C 8478 2.51 5 N 2397 2.21 5 O 2491 1.98 5 H 13086 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26542 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6552 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 425, 6552 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 6590 Chain: "B" Number of atoms: 6599 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6567 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 4, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 425, 6567 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 4, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 6603 Chain: "D" Number of atoms: 6633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6601 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 425, 6601 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 6639 Chain: "C" Number of atoms: 6634 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6602 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 425, 6602 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 6640 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AALA A 220 " occ=0.57 ... (18 atoms not shown) pdb=" HB3BALA A 220 " occ=0.43 residue: pdb=" N AALA B 220 " occ=0.57 ... (18 atoms not shown) pdb=" HB3BALA B 220 " occ=0.43 residue: pdb=" N AALA D 220 " occ=0.57 ... (18 atoms not shown) pdb=" HB3BALA D 220 " occ=0.43 residue: pdb=" N AALA C 220 " occ=0.57 ... (18 atoms not shown) pdb=" HB3BALA C 220 " occ=0.43 Time building chain proxies: 8.07, per 1000 atoms: 0.30 Number of scatterers: 26542 At special positions: 0 Unit cell: (103.653, 103.653, 105.747, 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) S 86 16.00 P 4 15.00 O 2491 8.00 N 2397 7.00 C 8478 6.00 H 13086 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.4 seconds 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 24 sheets defined 23.9% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 11 through 16 removed outlier: 3.789A pdb=" N GLN A 15 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 11 through 16' Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.605A pdb=" N ASN A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N CYS A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 92 through 96 removed outlier: 3.538A pdb=" N ASN A 96 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.691A pdb=" N TYR A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 127 through 132' Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.659A pdb=" N MET A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 220 through 232 removed outlier: 3.906A pdb=" N GLU A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 removed outlier: 3.718A pdb=" N LYS A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 292 removed outlier: 4.137A pdb=" N LEU A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 removed outlier: 4.132A pdb=" N ARG A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'B' and resid 11 through 16 removed outlier: 3.551A pdb=" N GLN B 15 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 16' Processing helix chain 'B' and resid 41 through 44 Processing helix chain 'B' and resid 55 through 64 removed outlier: 3.669A pdb=" N ASN B 60 " --> pdb=" O PHE B 56 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N CYS B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 148 through 159 removed outlier: 3.581A pdb=" N MET B 152 " --> pdb=" O ASP B 148 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.931A pdb=" N GLU B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 250 removed outlier: 3.716A pdb=" N LYS B 247 " --> pdb=" O ASP B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 289 removed outlier: 3.520A pdb=" N TYR B 283 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 418 through 424 Processing helix chain 'D' and resid 11 through 16 removed outlier: 3.656A pdb=" N GLN D 15 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 11 through 16' Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.624A pdb=" N LYS D 34 " --> pdb=" O THR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 44 Processing helix chain 'D' and resid 55 through 64 removed outlier: 3.561A pdb=" N ASN D 60 " --> pdb=" O PHE D 56 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N CYS D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 Processing helix chain 'D' and resid 92 through 96 removed outlier: 3.519A pdb=" N ASN D 96 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 148 through 159 removed outlier: 3.683A pdb=" N MET D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE D 154 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 220 through 232 removed outlier: 3.997A pdb=" N GLU D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 250 removed outlier: 3.751A pdb=" N LYS D 247 " --> pdb=" O ASP D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 289 removed outlier: 3.511A pdb=" N ASP D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 404 Processing helix chain 'D' and resid 418 through 424 Processing helix chain 'C' and resid 11 through 16 removed outlier: 3.533A pdb=" N LEU C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 44 Processing helix chain 'C' and resid 55 through 63 removed outlier: 3.574A pdb=" N ASN C 60 " --> pdb=" O PHE C 56 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N CYS C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 92 through 96 removed outlier: 3.530A pdb=" N ASN C 96 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 151 through 158 removed outlier: 3.763A pdb=" N ASP C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 228 removed outlier: 3.998A pdb=" N GLU C 225 " --> pdb=" O ASP C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 251 removed outlier: 4.345A pdb=" N ILE C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 279 through 292 removed outlier: 3.594A pdb=" N TYR C 283 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 291 " --> pdb=" O ASN C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'C' and resid 418 through 424 Processing sheet with id=A, first strand: chain 'A' and resid 98 through 101 removed outlier: 7.124A pdb=" N SER A 20 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N GLY A 70 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA A 22 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR A 135 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU A 23 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 137 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 215 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 167 through 171 Processing sheet with id=C, first strand: chain 'A' and resid 179 through 182 removed outlier: 3.544A pdb=" N GLU A 191 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=E, first strand: chain 'A' and resid 344 through 346 Processing sheet with id=F, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.696A pdb=" N CYS A 382 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A 415 " --> pdb=" O VAL A 383 " (cutoff:3.500A) No H-bonds generated for sheet with id=F Processing sheet with id=G, first strand: chain 'B' and resid 98 through 101 removed outlier: 7.296A pdb=" N SER B 20 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N GLY B 70 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA B 22 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR B 135 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU B 23 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 137 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE B 215 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'B' and resid 167 through 171 Processing sheet with id=I, first strand: chain 'B' and resid 179 through 182 Processing sheet with id=J, first strand: chain 'B' and resid 317 through 319 Processing sheet with id=K, first strand: chain 'B' and resid 344 through 346 Processing sheet with id=L, first strand: chain 'B' and resid 365 through 367 removed outlier: 6.746A pdb=" N CYS B 382 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 415 " --> pdb=" O VAL B 383 " (cutoff:3.500A) No H-bonds generated for sheet with id=L Processing sheet with id=M, first strand: chain 'D' and resid 98 through 101 removed outlier: 7.234A pdb=" N SER D 20 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N GLY D 70 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA D 22 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYR D 135 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU D 23 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL D 137 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE D 215 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'D' and resid 167 through 171 Processing sheet with id=O, first strand: chain 'D' and resid 179 through 182 removed outlier: 3.523A pdb=" N GLU D 191 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'D' and resid 317 through 319 Processing sheet with id=Q, first strand: chain 'D' and resid 344 through 346 Processing sheet with id=R, first strand: chain 'D' and resid 365 through 367 removed outlier: 6.734A pdb=" N CYS D 382 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL D 415 " --> pdb=" O VAL D 383 " (cutoff:3.500A) No H-bonds generated for sheet with id=R Processing sheet with id=S, first strand: chain 'C' and resid 98 through 101 removed outlier: 7.220A pdb=" N SER C 20 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N GLY C 70 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA C 22 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR C 135 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU C 23 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 137 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE C 215 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'C' and resid 167 through 171 Processing sheet with id=U, first strand: chain 'C' and resid 179 through 182 removed outlier: 3.577A pdb=" N GLU C 191 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'C' and resid 317 through 319 Processing sheet with id=W, first strand: chain 'C' and resid 344 through 346 Processing sheet with id=X, first strand: chain 'C' and resid 365 through 367 removed outlier: 6.701A pdb=" N CYS C 382 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 415 " --> pdb=" O VAL C 383 " (cutoff:3.500A) No H-bonds generated for sheet with id=X 274 hydrogen bonds defined for protein. 771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.83 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13050 1.04 - 1.23: 1017 1.23 - 1.43: 4858 1.43 - 1.63: 7783 1.63 - 1.82: 136 Bond restraints: 26844 Sorted by residual: bond pdb=" N VAL C 277 " pdb=" CA VAL C 277 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.32e+00 bond pdb=" N MET D 11 " pdb=" CA MET D 11 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 8.06e+00 bond pdb=" N VAL D 277 " pdb=" CA VAL D 277 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.53e+00 bond pdb=" N VAL B 277 " pdb=" CA VAL B 277 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.44e+00 bond pdb=" N HIS D 9 " pdb=" CA HIS D 9 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.27e-02 6.20e+03 7.36e+00 ... (remaining 26839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 43148 2.26 - 4.52: 4934 4.52 - 6.78: 308 6.78 - 9.04: 18 9.04 - 11.30: 5 Bond angle restraints: 48413 Sorted by residual: angle pdb=" C LEU B 33 " pdb=" N LYS B 34 " pdb=" CA LYS B 34 " ideal model delta sigma weight residual 121.54 130.34 -8.80 1.91e+00 2.74e-01 2.12e+01 angle pdb=" C LEU A 33 " pdb=" N LYS A 34 " pdb=" CA LYS A 34 " ideal model delta sigma weight residual 121.54 130.06 -8.52 1.91e+00 2.74e-01 1.99e+01 angle pdb=" C LEU D 33 " pdb=" N LYS D 34 " pdb=" CA LYS D 34 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C HIS C 9 " pdb=" N LEU C 10 " pdb=" CA LEU C 10 " ideal model delta sigma weight residual 120.54 126.45 -5.91 1.35e+00 5.49e-01 1.92e+01 angle pdb=" C LEU C 33 " pdb=" N LYS C 34 " pdb=" CA LYS C 34 " ideal model delta sigma weight residual 121.54 129.54 -8.00 1.91e+00 2.74e-01 1.75e+01 ... (remaining 48408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 11858 24.87 - 49.75: 710 49.75 - 74.62: 95 74.62 - 99.50: 4 99.50 - 124.37: 4 Dihedral angle restraints: 12671 sinusoidal: 6901 harmonic: 5770 Sorted by residual: dihedral pdb=" C5' AMP B 501 " pdb=" O5' AMP B 501 " pdb=" P AMP B 501 " pdb=" O3P AMP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 64.37 -124.37 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" C5' AMP D 501 " pdb=" O5' AMP D 501 " pdb=" P AMP D 501 " pdb=" O3P AMP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 64.30 -124.30 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" C5' AMP C 501 " pdb=" O5' AMP C 501 " pdb=" P AMP C 501 " pdb=" O3P AMP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 -173.36 113.36 1 2.00e+01 2.50e-03 3.35e+01 ... (remaining 12668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1532 0.081 - 0.161: 459 0.161 - 0.242: 58 0.242 - 0.323: 1 0.323 - 0.403: 2 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CG LEU D 36 " pdb=" CB LEU D 36 " pdb=" CD1 LEU D 36 " pdb=" CD2 LEU D 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CG LEU B 36 " pdb=" CB LEU B 36 " pdb=" CD1 LEU B 36 " pdb=" CD2 LEU B 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CG LEU A 12 " pdb=" CB LEU A 12 " pdb=" CD1 LEU A 12 " pdb=" CD2 LEU A 12 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2049 not shown) Planarity restraints: 4060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 407 " 0.007 2.00e-02 2.50e+03 3.87e-02 4.50e+01 pdb=" CG PHE B 407 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE B 407 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE B 407 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 407 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE B 407 " -0.041 2.00e-02 2.50e+03 pdb=" CZ PHE B 407 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 PHE B 407 " 0.041 2.00e-02 2.50e+03 pdb=" HD2 PHE B 407 " -0.038 2.00e-02 2.50e+03 pdb=" HE1 PHE B 407 " -0.079 2.00e-02 2.50e+03 pdb=" HE2 PHE B 407 " 0.057 2.00e-02 2.50e+03 pdb=" HZ PHE B 407 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 407 " -0.001 2.00e-02 2.50e+03 3.85e-02 4.44e+01 pdb=" CG PHE A 407 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 407 " -0.068 2.00e-02 2.50e+03 pdb=" CD2 PHE A 407 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE A 407 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 407 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 407 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 407 " 0.054 2.00e-02 2.50e+03 pdb=" HD2 PHE A 407 " -0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE A 407 " 0.027 2.00e-02 2.50e+03 pdb=" HE2 PHE A 407 " 0.062 2.00e-02 2.50e+03 pdb=" HZ PHE A 407 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 273 " -0.032 2.00e-02 2.50e+03 3.84e-02 4.43e+01 pdb=" CG TYR D 273 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR D 273 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR D 273 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR D 273 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR D 273 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR D 273 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR D 273 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR D 273 " 0.080 2.00e-02 2.50e+03 pdb=" HD2 TYR D 273 " 0.025 2.00e-02 2.50e+03 pdb=" HE1 TYR D 273 " -0.043 2.00e-02 2.50e+03 pdb=" HE2 TYR D 273 " 0.065 2.00e-02 2.50e+03 ... (remaining 4057 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 357 2.06 - 2.69: 42399 2.69 - 3.33: 74770 3.33 - 3.96: 101106 3.96 - 4.60: 160025 Nonbonded interactions: 378657 Sorted by model distance: nonbonded pdb=" HD2 TYR D 145 " pdb=" HE1 TRP D 274 " model vdw 1.425 2.100 nonbonded pdb="HD22 LEU B 33 " pdb="HD23 LEU B 36 " model vdw 1.461 2.440 nonbonded pdb="HG11 VAL A 277 " pdb=" HD1 TYR A 283 " model vdw 1.640 2.270 nonbonded pdb=" OD1 ASP A 184 " pdb=" H LYS A 188 " model vdw 1.651 2.450 nonbonded pdb="HH21 ARG B 386 " pdb=" O1P AMP B 501 " model vdw 1.672 2.450 ... (remaining 378652 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 7 through 111 or (resid 112 through 113 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 114 through \ 150 or resid 152 through 219 or resid 222 through 384 or (resid 385 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 386 \ through 501)) selection = (chain 'B' and (resid 7 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 30 through 106 or (resid \ 107 through 109 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 110 through 150 or resid 152 through 219 or resid 222 thr \ ough 266 or (resid 267 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 268 through 384 or (resid 385 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 386 through 5 \ 01)) selection = (chain 'C' and (resid 7 through 106 or (resid 107 through 109 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 110 through \ 111 or (resid 112 through 113 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 114 or (resid 115 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 116 through 150 o \ r resid 152 through 193 or (resid 194 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 195 through 219 or resid 222 throug \ h 266 or (resid 267 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 268 through 384 or (resid 385 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 386 through 501) \ ) selection = (chain 'D' and (resid 7 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 30 through 106 or (resid \ 107 through 109 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 110 through 111 or (resid 112 through 113 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 114 thro \ ugh 150 or resid 152 through 193 or (resid 194 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 195 through 219 or resid 2 \ 22 through 266 or (resid 267 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 268 through 501)) } 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=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.130 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 30.010 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.010 0.094 13758 Z= 0.501 Angle : 1.142 10.891 18678 Z= 0.633 Chirality : 0.073 0.403 2052 Planarity : 0.009 0.060 2436 Dihedral : 14.606 124.373 5126 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.33 % Favored : 91.31 % Rotamer: Outliers : 2.45 % Allowed : 8.13 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.17), residues: 1708 helix: -3.81 (0.15), residues: 412 sheet: -2.74 (0.25), residues: 336 loop : -1.79 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.005 ARG C 130 TYR 0.040 0.009 TYR A 273 PHE 0.047 0.011 PHE A 98 TRP 0.034 0.010 TRP C 274 HIS 0.033 0.007 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.01046 (13758) covalent geometry : angle 1.14226 (18678) hydrogen bonds : bond 0.24416 ( 274) hydrogen bonds : angle 10.28972 ( 771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 413 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 382 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7115 (mp10) REVERT: A 243 ASP cc_start: 0.7190 (m-30) cc_final: 0.6943 (m-30) REVERT: B 162 ARG cc_start: 0.7551 (mmm-85) cc_final: 0.7324 (mmm-85) REVERT: B 328 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6931 (mtm) REVERT: D 14 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8108 (ttp80) REVERT: D 82 GLN cc_start: 0.8197 (tt0) cc_final: 0.7602 (tt0) REVERT: D 92 ASN cc_start: 0.7729 (m-40) cc_final: 0.6906 (p0) REVERT: D 117 THR cc_start: 0.9046 (m) cc_final: 0.8645 (p) REVERT: D 184 ASP cc_start: 0.7777 (p0) cc_final: 0.6938 (p0) REVERT: D 187 ASP cc_start: 0.6681 (m-30) cc_final: 0.6480 (m-30) REVERT: D 341 SER cc_start: 0.8667 (m) cc_final: 0.8347 (t) REVERT: D 359 PHE cc_start: 0.8790 (m-80) cc_final: 0.8536 (m-80) REVERT: C 67 ARG cc_start: 0.8283 (mtp85) cc_final: 0.8061 (mtt90) REVERT: C 105 GLN cc_start: 0.7580 (mm110) cc_final: 0.7278 (mm110) REVERT: C 180 VAL cc_start: 0.9049 (t) cc_final: 0.8640 (m) REVERT: C 212 SER cc_start: 0.8773 (t) cc_final: 0.8093 (p) REVERT: C 309 TYR cc_start: 0.7945 (t80) cc_final: 0.7582 (t80) outliers start: 31 outliers final: 7 residues processed: 397 average time/residue: 0.3519 time to fit residues: 186.1682 Evaluate side-chains 232 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 223 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 328 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 9 HIS B 235 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN D 123 GLN C 9 HIS C 76 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.173890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141338 restraints weight = 87329.676| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.93 r_work: 0.3568 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13758 Z= 0.130 Angle : 0.670 7.238 18678 Z= 0.341 Chirality : 0.047 0.161 2052 Planarity : 0.006 0.059 2436 Dihedral : 8.211 93.298 1965 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Rotamer: Outliers : 1.68 % Allowed : 12.47 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.18), residues: 1708 helix: -2.35 (0.21), residues: 412 sheet: -1.56 (0.35), residues: 188 loop : -1.55 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 32 TYR 0.015 0.001 TYR C 75 PHE 0.018 0.002 PHE D 178 TRP 0.016 0.001 TRP A 284 HIS 0.008 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00284 (13758) covalent geometry : angle 0.66991 (18678) hydrogen bonds : bond 0.04971 ( 274) hydrogen bonds : angle 6.13316 ( 771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8548 (mtt180) cc_final: 0.8125 (mtm180) REVERT: A 123 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7275 (mp10) REVERT: A 243 ASP cc_start: 0.7521 (m-30) cc_final: 0.7278 (m-30) REVERT: A 296 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7498 (mt-10) REVERT: B 19 LYS cc_start: 0.7927 (mttt) cc_final: 0.7609 (mtmt) REVERT: B 34 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8645 (mmmm) REVERT: B 406 ARG cc_start: 0.8974 (mtp180) cc_final: 0.8540 (mtm180) REVERT: B 421 MET cc_start: 0.8178 (mtt) cc_final: 0.7937 (mtt) REVERT: D 11 MET cc_start: 0.8322 (mmm) cc_final: 0.8029 (tpp) REVERT: D 14 ARG cc_start: 0.8489 (ttp80) cc_final: 0.8223 (ttp80) REVERT: D 117 THR cc_start: 0.8943 (m) cc_final: 0.8503 (p) REVERT: D 328 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7052 (mtt) REVERT: D 341 SER cc_start: 0.8785 (m) cc_final: 0.8481 (t) REVERT: D 421 MET cc_start: 0.8127 (mtt) cc_final: 0.7835 (mtt) REVERT: C 14 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8203 (ttp80) REVERT: C 155 ASP cc_start: 0.8611 (m-30) cc_final: 0.7947 (m-30) REVERT: C 180 VAL cc_start: 0.8439 (t) cc_final: 0.8016 (m) REVERT: C 212 SER cc_start: 0.9081 (t) cc_final: 0.8453 (p) outliers start: 20 outliers final: 12 residues processed: 249 average time/residue: 0.2969 time to fit residues: 104.5385 Evaluate side-chains 224 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 126 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 19 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 126 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.169389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136383 restraints weight = 94431.755| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 4.26 r_work: 0.3492 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13758 Z= 0.143 Angle : 0.600 6.821 18678 Z= 0.300 Chirality : 0.047 0.150 2052 Planarity : 0.005 0.038 2436 Dihedral : 7.348 81.949 1957 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.43 % Favored : 95.51 % Rotamer: Outliers : 1.54 % Allowed : 13.03 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.19), residues: 1708 helix: -1.65 (0.24), residues: 424 sheet: -1.41 (0.35), residues: 188 loop : -1.40 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 380 TYR 0.017 0.001 TYR C 75 PHE 0.012 0.001 PHE D 178 TRP 0.012 0.001 TRP B 284 HIS 0.006 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00326 (13758) covalent geometry : angle 0.60040 (18678) hydrogen bonds : bond 0.03900 ( 274) hydrogen bonds : angle 5.38367 ( 771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 221 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: A 296 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 34 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8681 (mmmm) REVERT: B 97 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: B 202 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8180 (ttp) REVERT: D 11 MET cc_start: 0.8346 (mmm) cc_final: 0.8041 (tpp) REVERT: D 14 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8261 (ttp80) REVERT: D 174 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7564 (tm-30) REVERT: D 289 ASP cc_start: 0.8664 (t70) cc_final: 0.8323 (t0) REVERT: D 328 MET cc_start: 0.7439 (mtm) cc_final: 0.7071 (mtt) REVERT: D 341 SER cc_start: 0.8819 (m) cc_final: 0.8499 (t) REVERT: D 359 PHE cc_start: 0.9118 (m-80) cc_final: 0.8850 (m-80) REVERT: C 14 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8237 (ttp80) REVERT: C 34 LYS cc_start: 0.9376 (mmtt) cc_final: 0.9044 (mmmm) REVERT: C 180 VAL cc_start: 0.8605 (t) cc_final: 0.8318 (p) REVERT: C 212 SER cc_start: 0.9109 (t) cc_final: 0.8564 (p) REVERT: C 309 TYR cc_start: 0.8548 (t80) cc_final: 0.8286 (t80) REVERT: C 403 ASP cc_start: 0.8403 (m-30) cc_final: 0.8039 (m-30) outliers start: 18 outliers final: 7 residues processed: 233 average time/residue: 0.2976 time to fit residues: 97.2900 Evaluate side-chains 211 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain C residue 59 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 143 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN B 204 ASN B 235 ASN D 347 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.164857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.131279 restraints weight = 102234.112| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 4.48 r_work: 0.3381 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13758 Z= 0.202 Angle : 0.613 6.542 18678 Z= 0.308 Chirality : 0.047 0.153 2052 Planarity : 0.005 0.055 2436 Dihedral : 6.818 69.132 1948 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.32 % Favored : 94.62 % Rotamer: Outliers : 1.96 % Allowed : 13.38 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.19), residues: 1708 helix: -1.30 (0.25), residues: 428 sheet: -1.39 (0.34), residues: 188 loop : -1.33 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 322 TYR 0.022 0.001 TYR D 131 PHE 0.012 0.001 PHE A 192 TRP 0.011 0.001 TRP B 284 HIS 0.003 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00454 (13758) covalent geometry : angle 0.61324 (18678) hydrogen bonds : bond 0.03527 ( 274) hydrogen bonds : angle 5.13895 ( 771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8290 (pt0) REVERT: A 340 ILE cc_start: 0.9111 (mp) cc_final: 0.8874 (mm) REVERT: B 34 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8827 (mmmm) REVERT: B 202 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8221 (ttp) REVERT: D 174 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7225 (tm-30) REVERT: D 289 ASP cc_start: 0.8742 (t70) cc_final: 0.8428 (t0) REVERT: D 328 MET cc_start: 0.7612 (mtm) cc_final: 0.7248 (mtt) REVERT: D 341 SER cc_start: 0.8858 (m) cc_final: 0.8531 (t) REVERT: D 359 PHE cc_start: 0.9178 (m-80) cc_final: 0.8895 (m-80) REVERT: C 14 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8372 (ttp80) REVERT: C 34 LYS cc_start: 0.9366 (mmtt) cc_final: 0.9070 (mmmm) REVERT: C 212 SER cc_start: 0.9266 (t) cc_final: 0.8764 (p) REVERT: C 309 TYR cc_start: 0.8610 (t80) cc_final: 0.8381 (t80) REVERT: C 403 ASP cc_start: 0.8486 (m-30) cc_final: 0.8162 (m-30) outliers start: 24 outliers final: 17 residues processed: 215 average time/residue: 0.2926 time to fit residues: 88.6759 Evaluate side-chains 204 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 102 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.163288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130674 restraints weight = 86627.352| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.80 r_work: 0.3397 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13758 Z= 0.178 Angle : 0.588 6.362 18678 Z= 0.292 Chirality : 0.047 0.152 2052 Planarity : 0.004 0.039 2436 Dihedral : 6.554 58.921 1948 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.85 % Favored : 94.09 % Rotamer: Outliers : 1.82 % Allowed : 13.88 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.19), residues: 1708 helix: -1.00 (0.26), residues: 428 sheet: -1.26 (0.34), residues: 188 loop : -1.23 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 32 TYR 0.015 0.001 TYR C 75 PHE 0.011 0.001 PHE A 192 TRP 0.011 0.001 TRP B 284 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00410 (13758) covalent geometry : angle 0.58808 (18678) hydrogen bonds : bond 0.03273 ( 274) hydrogen bonds : angle 5.01432 ( 771) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: B 34 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8832 (mmmm) REVERT: B 86 ARG cc_start: 0.8915 (mtt-85) cc_final: 0.8672 (mtt-85) REVERT: B 97 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8157 (pm20) REVERT: B 355 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7730 (tpp-160) REVERT: D 174 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7301 (tm-30) REVERT: D 194 GLU cc_start: 0.6706 (tm-30) cc_final: 0.6321 (tm-30) REVERT: D 289 ASP cc_start: 0.8695 (t70) cc_final: 0.8391 (t0) REVERT: D 328 MET cc_start: 0.7667 (mtm) cc_final: 0.7316 (mtt) REVERT: D 341 SER cc_start: 0.8856 (m) cc_final: 0.8522 (t) REVERT: D 359 PHE cc_start: 0.9120 (m-80) cc_final: 0.8820 (m-80) REVERT: C 14 ARG cc_start: 0.8601 (ttp80) cc_final: 0.8309 (ttp80) REVERT: C 34 LYS cc_start: 0.9363 (mmtt) cc_final: 0.9043 (mmmm) REVERT: C 212 SER cc_start: 0.9238 (t) cc_final: 0.8737 (p) REVERT: C 309 TYR cc_start: 0.8545 (t80) cc_final: 0.8285 (t80) REVERT: C 403 ASP cc_start: 0.8453 (m-30) cc_final: 0.8225 (m-30) REVERT: C 421 MET cc_start: 0.8673 (mtt) cc_final: 0.8349 (mtt) REVERT: C 428 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8225 (tttm) REVERT: C 430 GLU cc_start: 0.7186 (mp0) cc_final: 0.6700 (mp0) outliers start: 22 outliers final: 16 residues processed: 207 average time/residue: 0.3270 time to fit residues: 96.9299 Evaluate side-chains 201 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 99 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.162934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129869 restraints weight = 94809.144| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 4.28 r_work: 0.3414 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13758 Z= 0.154 Angle : 0.571 6.097 18678 Z= 0.282 Chirality : 0.046 0.150 2052 Planarity : 0.004 0.040 2436 Dihedral : 6.336 59.432 1948 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.79 % Favored : 94.15 % Rotamer: Outliers : 1.75 % Allowed : 14.23 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.20), residues: 1708 helix: -0.81 (0.26), residues: 428 sheet: -1.25 (0.33), residues: 196 loop : -1.16 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 32 TYR 0.020 0.001 TYR D 114 PHE 0.011 0.001 PHE D 218 TRP 0.010 0.001 TRP B 284 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00354 (13758) covalent geometry : angle 0.57093 (18678) hydrogen bonds : bond 0.03067 ( 274) hydrogen bonds : angle 4.87498 ( 771) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8385 (pt0) REVERT: B 34 LYS cc_start: 0.9148 (mmtt) cc_final: 0.8845 (mmmm) REVERT: B 86 ARG cc_start: 0.8922 (mtt-85) cc_final: 0.8688 (mtt-85) REVERT: B 97 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: D 174 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7298 (tm-30) REVERT: D 194 GLU cc_start: 0.6755 (tm-30) cc_final: 0.6366 (tm-30) REVERT: D 289 ASP cc_start: 0.8659 (t70) cc_final: 0.8356 (t0) REVERT: D 328 MET cc_start: 0.7752 (mtm) cc_final: 0.7420 (mtt) REVERT: D 341 SER cc_start: 0.8840 (m) cc_final: 0.8550 (t) REVERT: D 359 PHE cc_start: 0.9073 (m-80) cc_final: 0.8768 (m-80) REVERT: D 380 ARG cc_start: 0.8545 (ttm-80) cc_final: 0.8175 (ttm-80) REVERT: D 398 GLU cc_start: 0.7349 (mp0) cc_final: 0.7138 (mp0) REVERT: C 14 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8327 (ttp80) REVERT: C 34 LYS cc_start: 0.9369 (mmtt) cc_final: 0.9068 (mmmm) REVERT: C 212 SER cc_start: 0.9246 (t) cc_final: 0.8747 (p) REVERT: C 428 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8245 (tttm) REVERT: C 430 GLU cc_start: 0.7143 (mp0) cc_final: 0.6679 (mp0) outliers start: 21 outliers final: 15 residues processed: 199 average time/residue: 0.2748 time to fit residues: 78.5160 Evaluate side-chains 195 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 311 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.161422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131697 restraints weight = 98236.228| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.80 r_work: 0.3403 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13758 Z= 0.235 Angle : 0.609 5.936 18678 Z= 0.306 Chirality : 0.048 0.148 2052 Planarity : 0.004 0.039 2436 Dihedral : 6.441 62.864 1948 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.10 % Favored : 91.84 % Rotamer: Outliers : 2.17 % Allowed : 14.09 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.20), residues: 1708 helix: -0.76 (0.26), residues: 416 sheet: -1.29 (0.33), residues: 196 loop : -1.27 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.016 0.002 TYR C 75 PHE 0.015 0.002 PHE A 192 TRP 0.012 0.002 TRP B 284 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00534 (13758) covalent geometry : angle 0.60918 (18678) hydrogen bonds : bond 0.03358 ( 274) hydrogen bonds : angle 5.07075 ( 771) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8370 (pt0) REVERT: A 299 MET cc_start: 0.8306 (mmm) cc_final: 0.7956 (mmm) REVERT: B 34 LYS cc_start: 0.9154 (mmtt) cc_final: 0.8894 (mmmm) REVERT: D 174 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7549 (tm-30) REVERT: D 194 GLU cc_start: 0.6716 (tm-30) cc_final: 0.6425 (tm-30) REVERT: D 289 ASP cc_start: 0.8709 (t70) cc_final: 0.8462 (t0) REVERT: D 328 MET cc_start: 0.7882 (mtm) cc_final: 0.7559 (mtt) REVERT: D 341 SER cc_start: 0.8793 (m) cc_final: 0.8576 (t) REVERT: D 380 ARG cc_start: 0.8543 (ttm-80) cc_final: 0.8192 (ttm-80) REVERT: C 212 SER cc_start: 0.9261 (t) cc_final: 0.8834 (p) REVERT: C 309 TYR cc_start: 0.8663 (t80) cc_final: 0.8412 (t80) REVERT: C 428 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8362 (tttm) outliers start: 27 outliers final: 19 residues processed: 200 average time/residue: 0.2886 time to fit residues: 82.2086 Evaluate side-chains 195 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN B 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.164790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133117 restraints weight = 97881.920| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.84 r_work: 0.3421 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13758 Z= 0.121 Angle : 0.558 6.009 18678 Z= 0.274 Chirality : 0.046 0.149 2052 Planarity : 0.004 0.059 2436 Dihedral : 6.215 60.550 1948 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.08 % Favored : 94.86 % Rotamer: Outliers : 1.47 % Allowed : 14.58 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.20), residues: 1708 helix: -0.44 (0.27), residues: 416 sheet: -1.14 (0.33), residues: 196 loop : -1.09 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 86 TYR 0.016 0.001 TYR D 114 PHE 0.010 0.001 PHE D 218 TRP 0.009 0.001 TRP B 284 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00282 (13758) covalent geometry : angle 0.55817 (18678) hydrogen bonds : bond 0.02917 ( 274) hydrogen bonds : angle 4.77639 ( 771) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: A 328 MET cc_start: 0.8144 (mmm) cc_final: 0.7339 (mmt) REVERT: B 34 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8823 (mmmm) REVERT: D 174 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7438 (tm-30) REVERT: D 194 GLU cc_start: 0.6734 (tm-30) cc_final: 0.6432 (tm-30) REVERT: D 289 ASP cc_start: 0.8701 (t70) cc_final: 0.8360 (t0) REVERT: D 328 MET cc_start: 0.7759 (mtm) cc_final: 0.7418 (mtt) REVERT: D 341 SER cc_start: 0.8772 (m) cc_final: 0.8530 (t) REVERT: D 380 ARG cc_start: 0.8554 (ttm-80) cc_final: 0.8224 (ttm-80) REVERT: C 212 SER cc_start: 0.9307 (t) cc_final: 0.8797 (p) REVERT: C 309 TYR cc_start: 0.8661 (t80) cc_final: 0.8390 (t80) REVERT: C 428 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8335 (tttm) outliers start: 17 outliers final: 12 residues processed: 198 average time/residue: 0.2662 time to fit residues: 76.0517 Evaluate side-chains 191 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 142 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.166676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135143 restraints weight = 100057.743| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.85 r_work: 0.3473 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13758 Z= 0.098 Angle : 0.546 5.881 18678 Z= 0.266 Chirality : 0.045 0.146 2052 Planarity : 0.004 0.051 2436 Dihedral : 6.003 57.670 1948 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.20 % Favored : 94.74 % Rotamer: Outliers : 1.33 % Allowed : 14.86 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.20), residues: 1708 helix: -0.15 (0.28), residues: 416 sheet: -0.95 (0.33), residues: 196 loop : -0.95 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 86 TYR 0.013 0.001 TYR D 114 PHE 0.017 0.001 PHE C 91 TRP 0.008 0.001 TRP B 284 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00229 (13758) covalent geometry : angle 0.54605 (18678) hydrogen bonds : bond 0.02678 ( 274) hydrogen bonds : angle 4.60296 ( 771) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8345 (pt0) REVERT: A 328 MET cc_start: 0.8182 (mmm) cc_final: 0.7344 (mmt) REVERT: B 34 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8836 (mmmm) REVERT: B 411 GLU cc_start: 0.8483 (tp30) cc_final: 0.7976 (tp30) REVERT: D 108 MET cc_start: 0.3686 (mmm) cc_final: 0.3438 (mmm) REVERT: D 174 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7371 (tm-30) REVERT: D 194 GLU cc_start: 0.6680 (tm-30) cc_final: 0.6290 (tm-30) REVERT: D 289 ASP cc_start: 0.8691 (t70) cc_final: 0.8347 (t0) REVERT: D 328 MET cc_start: 0.7808 (mtm) cc_final: 0.7508 (mtt) REVERT: D 341 SER cc_start: 0.8701 (m) cc_final: 0.8483 (t) REVERT: D 380 ARG cc_start: 0.8538 (ttm-80) cc_final: 0.8224 (ttm-80) REVERT: C 212 SER cc_start: 0.9289 (t) cc_final: 0.8761 (p) REVERT: C 309 TYR cc_start: 0.8605 (t80) cc_final: 0.8332 (t80) REVERT: C 428 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8343 (tttm) outliers start: 16 outliers final: 10 residues processed: 194 average time/residue: 0.2964 time to fit residues: 81.7147 Evaluate side-chains 190 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 133 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 94 optimal weight: 0.0170 chunk 14 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 overall best weight: 1.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.164740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134716 restraints weight = 92324.511| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.79 r_work: 0.3411 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13758 Z= 0.155 Angle : 0.563 5.683 18678 Z= 0.276 Chirality : 0.046 0.145 2052 Planarity : 0.004 0.059 2436 Dihedral : 6.019 58.026 1948 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.09 % Favored : 93.85 % Rotamer: Outliers : 1.05 % Allowed : 15.21 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.20), residues: 1708 helix: -0.15 (0.27), residues: 416 sheet: -0.88 (0.33), residues: 196 loop : -0.97 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 86 TYR 0.015 0.001 TYR C 75 PHE 0.011 0.001 PHE C 91 TRP 0.010 0.001 TRP B 284 HIS 0.003 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00358 (13758) covalent geometry : angle 0.56300 (18678) hydrogen bonds : bond 0.02866 ( 274) hydrogen bonds : angle 4.65815 ( 771) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8389 (pt0) REVERT: A 325 SER cc_start: 0.8989 (t) cc_final: 0.8771 (p) REVERT: A 328 MET cc_start: 0.8244 (mmm) cc_final: 0.7476 (mmt) REVERT: B 34 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8837 (mmmm) REVERT: D 194 GLU cc_start: 0.6697 (tm-30) cc_final: 0.6361 (tm-30) REVERT: D 289 ASP cc_start: 0.8713 (t70) cc_final: 0.8434 (t0) REVERT: D 328 MET cc_start: 0.7860 (mtm) cc_final: 0.7561 (mtt) REVERT: D 380 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8264 (ttm-80) REVERT: C 212 SER cc_start: 0.9255 (t) cc_final: 0.8809 (p) REVERT: C 301 ASP cc_start: 0.8059 (t0) cc_final: 0.7816 (t0) REVERT: C 309 TYR cc_start: 0.8654 (t80) cc_final: 0.8388 (t80) REVERT: C 428 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8378 (tttm) outliers start: 12 outliers final: 9 residues processed: 183 average time/residue: 0.2869 time to fit residues: 74.8261 Evaluate side-chains 181 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 123 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 150 optimal weight: 0.0270 chunk 143 optimal weight: 0.0980 chunk 95 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 142 optimal weight: 0.0470 chunk 42 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.164677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131194 restraints weight = 98417.590| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 4.33 r_work: 0.3405 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13758 Z= 0.090 Angle : 0.543 5.843 18678 Z= 0.262 Chirality : 0.045 0.144 2052 Planarity : 0.004 0.057 2436 Dihedral : 5.855 56.628 1948 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.98 % Allowed : 15.35 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.21), residues: 1708 helix: 0.11 (0.28), residues: 416 sheet: -0.75 (0.34), residues: 196 loop : -0.82 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 86 TYR 0.013 0.001 TYR C 75 PHE 0.012 0.001 PHE C 91 TRP 0.008 0.001 TRP B 284 HIS 0.003 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00210 (13758) covalent geometry : angle 0.54268 (18678) hydrogen bonds : bond 0.02580 ( 274) hydrogen bonds : angle 4.52104 ( 771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5686.46 seconds wall clock time: 97 minutes 1.15 seconds (5821.15 seconds total)