Starting phenix.real_space_refine on Wed Mar 4 13:32:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pxd_20518/03_2026/6pxd_20518_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pxd_20518/03_2026/6pxd_20518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pxd_20518/03_2026/6pxd_20518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pxd_20518/03_2026/6pxd_20518.map" model { file = "/net/cci-nas-00/data/ceres_data/6pxd_20518/03_2026/6pxd_20518_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pxd_20518/03_2026/6pxd_20518_neut.cif" } resolution = 2.9 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= 0.003 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 90 5.16 5 Cl 3 4.86 5 C 9055 2.51 5 N 2255 2.21 5 O 2496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 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: 13899 Number of models: 1 Model: "" Number of chains: 13 Chain: "E" Number of atoms: 2751 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2797 Chain: "A" Number of atoms: 2751 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2797 Chain: "B" Number of atoms: 2751 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2797 Chain: "C" Number of atoms: 2751 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2797 Chain: "D" Number of atoms: 2751 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2797 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AARG E 75 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 75 " occ=0.50 residue: pdb=" N AARG A 75 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 75 " occ=0.50 residue: pdb=" N AARG B 75 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 75 " occ=0.50 residue: pdb=" N AARG C 75 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 75 " occ=0.50 residue: pdb=" N AARG D 75 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 75 " occ=0.50 Time building chain proxies: 5.84, per 1000 atoms: 0.42 Number of scatterers: 13899 At special positions: 0 Unit cell: (97.76, 99.84, 132.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 3 17.00 S 90 16.00 O 2496 8.00 N 2255 7.00 C 9055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.04 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG F 1 " - " ASN E 54 " " NAG G 1 " - " ASN A 54 " " NAG H 1 " - " ASN B 54 " " NAG I 1 " - " ASN C 54 " " NAG J 1 " - " ASN D 54 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 25 sheets defined 38.2% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'E' and resid 29 through 35 Processing helix chain 'E' and resid 87 through 90 removed outlier: 3.565A pdb=" N ALA E 90 " --> pdb=" O PRO E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 90' Processing helix chain 'E' and resid 102 through 109 removed outlier: 3.885A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 109 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 161 removed outlier: 4.519A pdb=" N ASN E 160 " --> pdb=" O ASP E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 243 removed outlier: 3.631A pdb=" N ILE E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 257 removed outlier: 3.892A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 286 Processing helix chain 'E' and resid 297 through 324 removed outlier: 3.655A pdb=" N TRP E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 363 removed outlier: 3.916A pdb=" N VAL E 344 " --> pdb=" O THR E 340 " (cutoff:3.500A) Proline residue: E 347 - end of helix removed outlier: 3.662A pdb=" N TRP E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'A' and resid 87 through 90 removed outlier: 3.564A pdb=" N ALA A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 102 through 109 removed outlier: 3.884A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 4.518A pdb=" N ASN A 160 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 removed outlier: 3.631A pdb=" N ILE A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.893A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 286 Processing helix chain 'A' and resid 297 through 324 removed outlier: 3.655A pdb=" N TRP A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 363 removed outlier: 3.917A pdb=" N VAL A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Proline residue: A 347 - end of helix removed outlier: 3.663A pdb=" N TRP A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 87 through 90 removed outlier: 3.566A pdb=" N ALA B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 90' Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.885A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 109 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 4.519A pdb=" N ASN B 160 " --> pdb=" O ASP B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 removed outlier: 3.631A pdb=" N ILE B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 257 removed outlier: 3.893A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 286 Processing helix chain 'B' and resid 297 through 324 removed outlier: 3.655A pdb=" N TRP B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 363 removed outlier: 3.917A pdb=" N VAL B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Proline residue: B 347 - end of helix removed outlier: 3.661A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 87 through 90 removed outlier: 3.565A pdb=" N ALA C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 102 through 109 removed outlier: 3.885A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 109 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 4.519A pdb=" N ASN C 160 " --> pdb=" O ASP C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 removed outlier: 3.631A pdb=" N ILE C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.892A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 286 Processing helix chain 'C' and resid 297 through 324 removed outlier: 3.655A pdb=" N TRP C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 363 removed outlier: 3.917A pdb=" N VAL C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) Proline residue: C 347 - end of helix removed outlier: 3.663A pdb=" N TRP C 358 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'D' and resid 87 through 90 removed outlier: 3.565A pdb=" N ALA D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 102 through 109 removed outlier: 3.885A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 161 removed outlier: 4.519A pdb=" N ASN D 160 " --> pdb=" O ASP D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 243 removed outlier: 3.630A pdb=" N ILE D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.892A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 286 Processing helix chain 'D' and resid 297 through 324 removed outlier: 3.656A pdb=" N TRP D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 363 removed outlier: 3.917A pdb=" N VAL D 344 " --> pdb=" O THR D 340 " (cutoff:3.500A) Proline residue: D 347 - end of helix removed outlier: 3.663A pdb=" N TRP D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 99 through 101 removed outlier: 4.242A pdb=" N LEU E 134 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N AARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE E 64 " --> pdb=" O AARG E 75 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 119 through 123 removed outlier: 6.345A pdb=" N VAL E 151 " --> pdb=" O LYS E 120 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA E 122 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR E 149 " --> pdb=" O ALA E 122 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N AARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE E 64 " --> pdb=" O AARG E 75 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AA4, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AA5, first strand: chain 'E' and resid 216 through 217 Processing sheet with id=AA6, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.241A pdb=" N LEU A 134 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N AARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A 64 " --> pdb=" O AARG A 75 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 119 through 123 removed outlier: 6.344A pdb=" N VAL A 151 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA A 122 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR A 149 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N AARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A 64 " --> pdb=" O AARG A 75 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA9, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AB1, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AB2, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.242A pdb=" N LEU B 134 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N AARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 64 " --> pdb=" O AARG B 75 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 119 through 123 removed outlier: 6.344A pdb=" N VAL B 151 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA B 122 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR B 149 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N AARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 64 " --> pdb=" O AARG B 75 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB5, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB6, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'C' and resid 99 through 101 removed outlier: 4.242A pdb=" N LEU C 134 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N AARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE C 64 " --> pdb=" O AARG C 75 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 119 through 123 removed outlier: 6.345A pdb=" N VAL C 151 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA C 122 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR C 149 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N AARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE C 64 " --> pdb=" O AARG C 75 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AC1, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AC2, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AC3, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.242A pdb=" N LEU D 134 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N AARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE D 64 " --> pdb=" O AARG D 75 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 119 through 123 removed outlier: 6.344A pdb=" N VAL D 151 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA D 122 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR D 149 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N AARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE D 64 " --> pdb=" O AARG D 75 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC6, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC7, first strand: chain 'D' and resid 216 through 217 805 hydrogen bonds defined for protein. 2335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4285 1.35 - 1.47: 3752 1.47 - 1.60: 6058 1.60 - 1.72: 0 1.72 - 1.85: 150 Bond restraints: 14245 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.55e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.49e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.42e+00 ... (remaining 14240 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 18475 2.21 - 4.41: 694 4.41 - 6.62: 126 6.62 - 8.83: 40 8.83 - 11.03: 10 Bond angle restraints: 19345 Sorted by residual: angle pdb=" N ALA B 345 " pdb=" CA ALA B 345 " pdb=" C ALA B 345 " ideal model delta sigma weight residual 111.28 121.40 -10.12 1.09e+00 8.42e-01 8.62e+01 angle pdb=" N ALA A 345 " pdb=" CA ALA A 345 " pdb=" C ALA A 345 " ideal model delta sigma weight residual 111.28 121.39 -10.11 1.09e+00 8.42e-01 8.60e+01 angle pdb=" N ALA D 345 " pdb=" CA ALA D 345 " pdb=" C ALA D 345 " ideal model delta sigma weight residual 111.28 121.38 -10.10 1.09e+00 8.42e-01 8.58e+01 angle pdb=" N ALA E 345 " pdb=" CA ALA E 345 " pdb=" C ALA E 345 " ideal model delta sigma weight residual 111.28 121.37 -10.09 1.09e+00 8.42e-01 8.58e+01 angle pdb=" N ALA C 345 " pdb=" CA ALA C 345 " pdb=" C ALA C 345 " ideal model delta sigma weight residual 111.28 121.37 -10.09 1.09e+00 8.42e-01 8.56e+01 ... (remaining 19340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 8173 15.77 - 31.53: 312 31.53 - 47.30: 105 47.30 - 63.06: 30 63.06 - 78.83: 10 Dihedral angle restraints: 8630 sinusoidal: 3590 harmonic: 5040 Sorted by residual: dihedral pdb=" CB CYS D 214 " pdb=" SG CYS D 214 " pdb=" SG CYS D 225 " pdb=" CB CYS D 225 " ideal model delta sinusoidal sigma weight residual -86.00 -164.83 78.83 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 225 " pdb=" CB CYS C 225 " ideal model delta sinusoidal sigma weight residual -86.00 -164.83 78.83 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 225 " pdb=" CB CYS A 225 " ideal model delta sinusoidal sigma weight residual -86.00 -164.82 78.82 1 1.00e+01 1.00e-02 7.74e+01 ... (remaining 8627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2015 0.096 - 0.192: 175 0.192 - 0.287: 0 0.287 - 0.383: 10 0.383 - 0.479: 5 Chirality restraints: 2205 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 54 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN E 54 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN D 54 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.64e+00 ... (remaining 2202 not shown) Planarity restraints: 2415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 128 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C THR B 128 " -0.044 2.00e-02 2.50e+03 pdb=" O THR B 128 " 0.016 2.00e-02 2.50e+03 pdb=" N THR B 129 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 128 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C THR A 128 " -0.044 2.00e-02 2.50e+03 pdb=" O THR A 128 " 0.016 2.00e-02 2.50e+03 pdb=" N THR A 129 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 128 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C THR D 128 " 0.044 2.00e-02 2.50e+03 pdb=" O THR D 128 " -0.016 2.00e-02 2.50e+03 pdb=" N THR D 129 " -0.015 2.00e-02 2.50e+03 ... (remaining 2412 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 395 2.70 - 3.25: 12981 3.25 - 3.80: 21915 3.80 - 4.35: 28725 4.35 - 4.90: 49609 Nonbonded interactions: 113625 Sorted by model distance: nonbonded pdb=" OD2 ASP E 41 " pdb=" OG SER A 27 " model vdw 2.154 3.040 nonbonded pdb=" OD2 ASP B 41 " pdb=" OG SER C 27 " model vdw 2.192 3.040 nonbonded pdb=" OD2 ASP C 41 " pdb=" OG SER D 27 " model vdw 2.195 3.040 nonbonded pdb=" O LEU C 106 " pdb=" NZ LYS C 111 " model vdw 2.233 3.120 nonbonded pdb=" O LEU E 106 " pdb=" NZ LYS E 111 " model vdw 2.233 3.120 ... (remaining 113620 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 25 through 74 or resid 76 through 364)) selection = (chain 'B' and (resid 25 through 74 or resid 76 through 364)) selection = (chain 'C' and (resid 25 through 74 or resid 76 through 364)) selection = (chain 'D' and (resid 25 through 74 or resid 76 through 364)) selection = (chain 'E' and (resid 25 through 74 or resid 76 through 364)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.50 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.400 Find NCS groups from input model: 0.320 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: 0.000 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14265 Z= 0.302 Angle : 1.081 11.033 19395 Z= 0.625 Chirality : 0.062 0.479 2205 Planarity : 0.008 0.062 2410 Dihedral : 10.489 70.313 5340 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.32 % Allowed : 2.65 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -3.03 (0.17), residues: 1705 helix: -2.32 (0.17), residues: 545 sheet: -0.84 (0.26), residues: 380 loop : -2.31 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 343 TYR 0.023 0.003 TYR C 144 PHE 0.029 0.003 PHE C 116 TRP 0.030 0.004 TRP C 110 HIS 0.004 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00684 (14245) covalent geometry : angle 1.04738 (19345) SS BOND : bond 0.00834 ( 10) SS BOND : angle 3.23389 ( 20) hydrogen bonds : bond 0.15986 ( 660) hydrogen bonds : angle 10.04226 ( 2335) link_BETA1-4 : bond 0.01199 ( 5) link_BETA1-4 : angle 4.02430 ( 15) link_NAG-ASN : bond 0.02911 ( 5) link_NAG-ASN : angle 8.09137 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 357 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: E 96 ASP cc_start: 0.6338 (p0) cc_final: 0.5993 (p0) REVERT: E 107 ASP cc_start: 0.8157 (m-30) cc_final: 0.7875 (m-30) REVERT: E 159 LYS cc_start: 0.8560 (tmmt) cc_final: 0.8180 (mmtt) REVERT: E 189 LYS cc_start: 0.8387 (tptp) cc_final: 0.8166 (tppp) REVERT: E 210 ASP cc_start: 0.7446 (t70) cc_final: 0.6987 (t70) REVERT: E 222 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8628 (mtmt) REVERT: E 279 MET cc_start: 0.8520 (tpp) cc_final: 0.8305 (tpt) REVERT: E 287 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7193 (mtt-85) REVERT: E 339 ASP cc_start: 0.5828 (t0) cc_final: 0.5479 (t0) REVERT: A 96 ASP cc_start: 0.6038 (p0) cc_final: 0.5812 (p0) REVERT: A 105 MET cc_start: 0.8006 (mmm) cc_final: 0.7710 (mmm) REVERT: A 107 ASP cc_start: 0.8073 (m-30) cc_final: 0.7857 (m-30) REVERT: A 159 LYS cc_start: 0.8575 (tmmt) cc_final: 0.8107 (mttm) REVERT: A 185 GLU cc_start: 0.7954 (pt0) cc_final: 0.7714 (mt-10) REVERT: A 227 GLU cc_start: 0.8322 (pt0) cc_final: 0.8119 (pt0) REVERT: A 279 MET cc_start: 0.8582 (tpp) cc_final: 0.8377 (tpt) REVERT: A 337 ARG cc_start: 0.6242 (OUTLIER) cc_final: 0.4921 (mtt180) REVERT: A 339 ASP cc_start: 0.5903 (t0) cc_final: 0.5615 (t0) REVERT: A 350 PHE cc_start: 0.8130 (t80) cc_final: 0.7552 (t80) REVERT: B 210 ASP cc_start: 0.7448 (t70) cc_final: 0.6946 (t0) REVERT: B 222 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8430 (ttmt) REVERT: B 337 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.4885 (mtp-110) REVERT: B 339 ASP cc_start: 0.5765 (t0) cc_final: 0.5524 (t0) REVERT: B 361 TYR cc_start: 0.8110 (m-80) cc_final: 0.7757 (m-80) REVERT: C 210 ASP cc_start: 0.7451 (t70) cc_final: 0.6971 (t70) REVERT: C 222 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8491 (ttmt) REVERT: C 279 MET cc_start: 0.8607 (tpp) cc_final: 0.8352 (mmm) REVERT: C 337 ARG cc_start: 0.5946 (OUTLIER) cc_final: 0.4804 (mtp180) REVERT: D 96 ASP cc_start: 0.6375 (p0) cc_final: 0.5502 (p0) REVERT: D 212 ARG cc_start: 0.7414 (mmt-90) cc_final: 0.7121 (mmp80) REVERT: D 337 ARG cc_start: 0.6445 (OUTLIER) cc_final: 0.5431 (mtt180) REVERT: D 350 PHE cc_start: 0.7977 (t80) cc_final: 0.7620 (t80) outliers start: 20 outliers final: 0 residues processed: 377 average time/residue: 0.5833 time to fit residues: 240.5125 Evaluate side-chains 194 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 222 LYS Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain D residue 337 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.0170 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.0060 chunk 149 optimal weight: 0.8980 overall best weight: 0.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 131 ASN E 231 HIS A 131 ASN A 231 HIS ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 ASN B 131 ASN B 231 HIS ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 131 ASN C 231 HIS C 242 GLN C 282 GLN D 47 ASN D 131 ASN D 231 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.104481 restraints weight = 56837.314| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.70 r_work: 0.3050 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14265 Z= 0.139 Angle : 0.733 14.228 19395 Z= 0.370 Chirality : 0.048 0.309 2205 Planarity : 0.006 0.054 2410 Dihedral : 6.606 57.768 2103 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.44 % Allowed : 10.93 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.49 (0.19), residues: 1705 helix: -0.28 (0.20), residues: 550 sheet: -0.73 (0.27), residues: 380 loop : -1.58 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 287 TYR 0.033 0.002 TYR D 317 PHE 0.020 0.002 PHE E 356 TRP 0.015 0.002 TRP E 259 HIS 0.004 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00297 (14245) covalent geometry : angle 0.69709 (19345) SS BOND : bond 0.00584 ( 10) SS BOND : angle 4.69188 ( 20) hydrogen bonds : bond 0.04297 ( 660) hydrogen bonds : angle 5.93737 ( 2335) link_BETA1-4 : bond 0.00193 ( 5) link_BETA1-4 : angle 1.08933 ( 15) link_NAG-ASN : bond 0.01942 ( 5) link_NAG-ASN : angle 6.17693 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 238 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 107 ASP cc_start: 0.8669 (m-30) cc_final: 0.8399 (m-30) REVERT: E 159 LYS cc_start: 0.8716 (tmmt) cc_final: 0.8218 (mttt) REVERT: E 189 LYS cc_start: 0.8520 (tptp) cc_final: 0.8267 (tppp) REVERT: E 214 CYS cc_start: 0.6814 (p) cc_final: 0.6534 (p) REVERT: E 242 GLN cc_start: 0.8100 (tp-100) cc_final: 0.7502 (tm-30) REVERT: E 253 LEU cc_start: 0.8414 (mt) cc_final: 0.8154 (mt) REVERT: E 329 LYS cc_start: 0.5282 (OUTLIER) cc_final: 0.4931 (pptt) REVERT: E 337 ARG cc_start: 0.6814 (tpp80) cc_final: 0.5261 (mtp180) REVERT: E 339 ASP cc_start: 0.6111 (t0) cc_final: 0.5701 (t0) REVERT: E 363 LEU cc_start: 0.7848 (tp) cc_final: 0.7453 (tt) REVERT: A 96 ASP cc_start: 0.6401 (p0) cc_final: 0.5690 (p0) REVERT: A 105 MET cc_start: 0.8318 (mmm) cc_final: 0.7913 (mmm) REVERT: A 159 LYS cc_start: 0.8695 (tmmt) cc_final: 0.8149 (mttm) REVERT: A 185 GLU cc_start: 0.8520 (pt0) cc_final: 0.8035 (mt-10) REVERT: A 227 GLU cc_start: 0.8794 (pt0) cc_final: 0.8557 (pt0) REVERT: A 243 MET cc_start: 0.8572 (mtm) cc_final: 0.8288 (mtt) REVERT: A 287 ARG cc_start: 0.7747 (ttm110) cc_final: 0.7464 (tpp80) REVERT: A 329 LYS cc_start: 0.5417 (OUTLIER) cc_final: 0.5198 (ptmt) REVERT: B 96 ASP cc_start: 0.6269 (p0) cc_final: 0.5453 (p0) REVERT: B 123 ASN cc_start: 0.8972 (p0) cc_final: 0.8770 (p0) REVERT: B 210 ASP cc_start: 0.7811 (t70) cc_final: 0.7568 (t70) REVERT: B 242 GLN cc_start: 0.8417 (mm-40) cc_final: 0.7343 (tm-30) REVERT: B 243 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7834 (mtt) REVERT: C 96 ASP cc_start: 0.6474 (p0) cc_final: 0.6051 (p0) REVERT: C 159 LYS cc_start: 0.8700 (tmmt) cc_final: 0.8285 (mttm) REVERT: C 179 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8419 (mtt) REVERT: C 210 ASP cc_start: 0.7733 (t70) cc_final: 0.7180 (t70) REVERT: C 279 MET cc_start: 0.8849 (tpp) cc_final: 0.8571 (mmm) REVERT: C 287 ARG cc_start: 0.7893 (ttm110) cc_final: 0.7247 (tpp80) REVERT: D 96 ASP cc_start: 0.6594 (p0) cc_final: 0.5609 (p0) REVERT: D 105 MET cc_start: 0.8357 (mmm) cc_final: 0.7638 (mmt) REVERT: D 159 LYS cc_start: 0.8554 (tmmt) cc_final: 0.8109 (mttm) REVERT: D 173 GLU cc_start: 0.8453 (tt0) cc_final: 0.8034 (tt0) REVERT: D 193 GLN cc_start: 0.8945 (mt0) cc_final: 0.8666 (mt0) REVERT: D 242 GLN cc_start: 0.8190 (tp-100) cc_final: 0.7572 (tm-30) REVERT: D 279 MET cc_start: 0.8791 (tpt) cc_final: 0.8176 (tpt) REVERT: D 314 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7673 (tt) REVERT: D 329 LYS cc_start: 0.5840 (OUTLIER) cc_final: 0.5441 (pptt) REVERT: D 350 PHE cc_start: 0.8247 (t80) cc_final: 0.8013 (t80) outliers start: 52 outliers final: 19 residues processed: 274 average time/residue: 0.5387 time to fit residues: 163.3973 Evaluate side-chains 213 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 144 optimal weight: 0.1980 chunk 164 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 GLN E 139 ASN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 GLN B 166 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN C 282 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.102103 restraints weight = 59218.695| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.80 r_work: 0.3012 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14265 Z= 0.163 Angle : 0.787 17.520 19395 Z= 0.390 Chirality : 0.048 0.287 2205 Planarity : 0.005 0.052 2410 Dihedral : 6.161 51.408 2075 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.84 % Allowed : 12.38 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.70 (0.20), residues: 1705 helix: 0.90 (0.22), residues: 545 sheet: -0.65 (0.26), residues: 385 loop : -1.33 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 287 TYR 0.018 0.002 TYR E 317 PHE 0.024 0.002 PHE E 356 TRP 0.015 0.002 TRP A 358 HIS 0.002 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00368 (14245) covalent geometry : angle 0.73981 (19345) SS BOND : bond 0.00947 ( 10) SS BOND : angle 6.37777 ( 20) hydrogen bonds : bond 0.03935 ( 660) hydrogen bonds : angle 5.39824 ( 2335) link_BETA1-4 : bond 0.00334 ( 5) link_BETA1-4 : angle 1.16846 ( 15) link_NAG-ASN : bond 0.01822 ( 5) link_NAG-ASN : angle 6.22621 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 197 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: E 107 ASP cc_start: 0.8622 (m-30) cc_final: 0.8361 (m-30) REVERT: E 159 LYS cc_start: 0.8712 (tmmt) cc_final: 0.8488 (tttp) REVERT: E 189 LYS cc_start: 0.8456 (tptp) cc_final: 0.8219 (tppp) REVERT: E 210 ASP cc_start: 0.7735 (t70) cc_final: 0.7153 (t70) REVERT: E 214 CYS cc_start: 0.6822 (p) cc_final: 0.6555 (p) REVERT: E 242 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7364 (tm-30) REVERT: E 253 LEU cc_start: 0.8522 (mt) cc_final: 0.8200 (mt) REVERT: E 287 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.7308 (mtt-85) REVERT: E 337 ARG cc_start: 0.6777 (tpp80) cc_final: 0.5348 (mtt180) REVERT: E 363 LEU cc_start: 0.7863 (tp) cc_final: 0.7443 (tt) REVERT: A 96 ASP cc_start: 0.6446 (p0) cc_final: 0.6182 (p0) REVERT: A 105 MET cc_start: 0.8335 (mmm) cc_final: 0.7949 (mmm) REVERT: A 159 LYS cc_start: 0.8671 (tmmt) cc_final: 0.8041 (mmtt) REVERT: A 185 GLU cc_start: 0.8456 (pt0) cc_final: 0.7985 (mt-10) REVERT: A 193 GLN cc_start: 0.8913 (mt0) cc_final: 0.8585 (mt0) REVERT: A 243 MET cc_start: 0.8533 (mtm) cc_final: 0.8253 (mtt) REVERT: A 329 LYS cc_start: 0.5346 (OUTLIER) cc_final: 0.5104 (ptmt) REVERT: B 53 VAL cc_start: 0.8462 (m) cc_final: 0.8262 (p) REVERT: B 96 ASP cc_start: 0.6280 (p0) cc_final: 0.5462 (p0) REVERT: B 188 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: B 210 ASP cc_start: 0.7799 (t70) cc_final: 0.7539 (t70) REVERT: B 242 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8150 (mm-40) REVERT: B 243 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7717 (mtt) REVERT: B 339 ASP cc_start: 0.6428 (OUTLIER) cc_final: 0.5767 (m-30) REVERT: B 361 TYR cc_start: 0.8405 (m-80) cc_final: 0.7496 (m-80) REVERT: C 96 ASP cc_start: 0.6664 (p0) cc_final: 0.6356 (p0) REVERT: C 179 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8455 (mtt) REVERT: C 210 ASP cc_start: 0.7782 (t70) cc_final: 0.7229 (t70) REVERT: C 279 MET cc_start: 0.8855 (tpp) cc_final: 0.8586 (mmm) REVERT: C 287 ARG cc_start: 0.7815 (ttm110) cc_final: 0.7614 (tpp80) REVERT: C 339 ASP cc_start: 0.6542 (OUTLIER) cc_final: 0.5971 (m-30) REVERT: D 96 ASP cc_start: 0.6820 (p0) cc_final: 0.6382 (p0) REVERT: D 105 MET cc_start: 0.8391 (mmm) cc_final: 0.7643 (mmt) REVERT: D 159 LYS cc_start: 0.8614 (tmmt) cc_final: 0.8147 (mttm) REVERT: D 166 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7546 (mp10) REVERT: D 173 GLU cc_start: 0.8270 (tt0) cc_final: 0.7715 (tt0) REVERT: D 185 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: D 193 GLN cc_start: 0.8939 (mt0) cc_final: 0.8672 (mt0) REVERT: D 242 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7852 (mm-40) REVERT: D 243 MET cc_start: 0.8507 (mtt) cc_final: 0.8217 (mtt) REVERT: D 277 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8259 (tt) REVERT: D 350 PHE cc_start: 0.8337 (t80) cc_final: 0.8073 (t80) outliers start: 58 outliers final: 30 residues processed: 237 average time/residue: 0.5299 time to fit residues: 139.0898 Evaluate side-chains 215 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 277 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 104 optimal weight: 0.2980 chunk 7 optimal weight: 0.3980 chunk 136 optimal weight: 2.9990 chunk 118 optimal weight: 0.0670 chunk 128 optimal weight: 0.3980 chunk 158 optimal weight: 0.8980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN E 282 GLN A 82 GLN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 282 GLN D 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.104808 restraints weight = 55379.128| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.74 r_work: 0.3043 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14265 Z= 0.124 Angle : 0.691 13.763 19395 Z= 0.343 Chirality : 0.045 0.269 2205 Planarity : 0.004 0.044 2410 Dihedral : 5.830 53.172 2075 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.25 % Allowed : 14.24 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.28 (0.21), residues: 1705 helix: 1.49 (0.22), residues: 560 sheet: -0.55 (0.26), residues: 385 loop : -1.26 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 287 TYR 0.027 0.001 TYR C 317 PHE 0.022 0.001 PHE C 356 TRP 0.011 0.001 TRP D 358 HIS 0.002 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00272 (14245) covalent geometry : angle 0.64502 (19345) SS BOND : bond 0.00558 ( 10) SS BOND : angle 5.47982 ( 20) hydrogen bonds : bond 0.03445 ( 660) hydrogen bonds : angle 4.90109 ( 2335) link_BETA1-4 : bond 0.00425 ( 5) link_BETA1-4 : angle 1.31810 ( 15) link_NAG-ASN : bond 0.01690 ( 5) link_NAG-ASN : angle 6.24800 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 100 ASP cc_start: 0.8430 (p0) cc_final: 0.7669 (m-30) REVERT: E 107 ASP cc_start: 0.8583 (m-30) cc_final: 0.8338 (m-30) REVERT: E 159 LYS cc_start: 0.8665 (tmmt) cc_final: 0.8149 (mttt) REVERT: E 189 LYS cc_start: 0.8439 (tptp) cc_final: 0.8162 (tppp) REVERT: E 210 ASP cc_start: 0.7686 (t70) cc_final: 0.7063 (t70) REVERT: E 214 CYS cc_start: 0.6795 (p) cc_final: 0.6470 (p) REVERT: E 242 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7665 (tm-30) REVERT: E 253 LEU cc_start: 0.8540 (mt) cc_final: 0.8202 (mt) REVERT: E 314 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7917 (tt) REVERT: E 337 ARG cc_start: 0.6587 (tpp80) cc_final: 0.5277 (mtt180) REVERT: E 339 ASP cc_start: 0.6277 (t0) cc_final: 0.5907 (t0) REVERT: E 363 LEU cc_start: 0.7771 (tp) cc_final: 0.7373 (tt) REVERT: A 96 ASP cc_start: 0.6301 (p0) cc_final: 0.6088 (p0) REVERT: A 105 MET cc_start: 0.8263 (mmm) cc_final: 0.7889 (mmm) REVERT: A 159 LYS cc_start: 0.8628 (tmmt) cc_final: 0.8021 (mttt) REVERT: A 166 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7333 (mp10) REVERT: A 185 GLU cc_start: 0.8367 (pt0) cc_final: 0.7979 (mt-10) REVERT: A 193 GLN cc_start: 0.8939 (mt0) cc_final: 0.8591 (mt0) REVERT: B 179 MET cc_start: 0.8936 (mtp) cc_final: 0.8653 (mmt) REVERT: B 188 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: B 210 ASP cc_start: 0.7791 (t70) cc_final: 0.7366 (t0) REVERT: B 212 ARG cc_start: 0.7745 (mmt-90) cc_final: 0.7486 (mmp80) REVERT: B 242 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7575 (tm-30) REVERT: B 243 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7567 (mtt) REVERT: B 339 ASP cc_start: 0.6450 (OUTLIER) cc_final: 0.5785 (m-30) REVERT: C 159 LYS cc_start: 0.8690 (tmmt) cc_final: 0.8181 (mttt) REVERT: C 210 ASP cc_start: 0.7837 (t70) cc_final: 0.7244 (t70) REVERT: C 279 MET cc_start: 0.8815 (tpp) cc_final: 0.8561 (mmm) REVERT: C 287 ARG cc_start: 0.7922 (ttm110) cc_final: 0.7633 (tpp80) REVERT: C 339 ASP cc_start: 0.6541 (OUTLIER) cc_final: 0.5979 (m-30) REVERT: C 363 LEU cc_start: 0.7578 (tp) cc_final: 0.7227 (mp) REVERT: D 96 ASP cc_start: 0.6737 (p0) cc_final: 0.6327 (p0) REVERT: D 159 LYS cc_start: 0.8649 (tmmt) cc_final: 0.8226 (mttm) REVERT: D 166 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: D 173 GLU cc_start: 0.8224 (tt0) cc_final: 0.7750 (tt0) REVERT: D 193 GLN cc_start: 0.8887 (mt0) cc_final: 0.8583 (mt0) REVERT: D 242 GLN cc_start: 0.8129 (tp-100) cc_final: 0.7623 (tm-30) REVERT: D 277 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8212 (tt) REVERT: D 314 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7156 (tt) REVERT: D 329 LYS cc_start: 0.5522 (OUTLIER) cc_final: 0.5152 (pptt) outliers start: 49 outliers final: 19 residues processed: 253 average time/residue: 0.5740 time to fit residues: 159.5286 Evaluate side-chains 207 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 162 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 164 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN E 282 GLN A 82 GLN A 242 GLN B 82 GLN C 82 GLN C 282 GLN D 82 GLN D 282 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.131676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.102305 restraints weight = 59525.715| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.80 r_work: 0.3026 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14265 Z= 0.151 Angle : 0.693 13.455 19395 Z= 0.345 Chirality : 0.046 0.265 2205 Planarity : 0.004 0.043 2410 Dihedral : 5.836 52.168 2075 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.65 % Allowed : 15.43 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.11 (0.21), residues: 1705 helix: 1.81 (0.22), residues: 560 sheet: -0.58 (0.26), residues: 385 loop : -1.24 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 287 TYR 0.019 0.002 TYR E 317 PHE 0.024 0.002 PHE C 356 TRP 0.014 0.001 TRP A 358 HIS 0.003 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00346 (14245) covalent geometry : angle 0.64883 (19345) SS BOND : bond 0.00619 ( 10) SS BOND : angle 5.34710 ( 20) hydrogen bonds : bond 0.03527 ( 660) hydrogen bonds : angle 4.78009 ( 2335) link_BETA1-4 : bond 0.00370 ( 5) link_BETA1-4 : angle 1.10932 ( 15) link_NAG-ASN : bond 0.01619 ( 5) link_NAG-ASN : angle 6.15823 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: E 100 ASP cc_start: 0.8452 (p0) cc_final: 0.7739 (m-30) REVERT: E 107 ASP cc_start: 0.8548 (m-30) cc_final: 0.8313 (m-30) REVERT: E 159 LYS cc_start: 0.8715 (tmmt) cc_final: 0.8511 (tttp) REVERT: E 189 LYS cc_start: 0.8470 (tptp) cc_final: 0.8218 (tppp) REVERT: E 210 ASP cc_start: 0.7743 (t70) cc_final: 0.7098 (t70) REVERT: E 214 CYS cc_start: 0.6739 (p) cc_final: 0.6483 (p) REVERT: E 242 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7647 (tm-30) REVERT: E 253 LEU cc_start: 0.8580 (mt) cc_final: 0.8211 (mt) REVERT: E 314 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7959 (tt) REVERT: E 337 ARG cc_start: 0.6240 (tpp80) cc_final: 0.5147 (mtt180) REVERT: E 339 ASP cc_start: 0.6403 (t0) cc_final: 0.5990 (t0) REVERT: A 105 MET cc_start: 0.8318 (mmm) cc_final: 0.7944 (mmm) REVERT: A 159 LYS cc_start: 0.8677 (tmmt) cc_final: 0.8143 (mttm) REVERT: A 185 GLU cc_start: 0.8388 (pt0) cc_final: 0.8011 (mt-10) REVERT: A 193 GLN cc_start: 0.8930 (mt0) cc_final: 0.8575 (mt0) REVERT: B 96 ASP cc_start: 0.6266 (p0) cc_final: 0.5522 (p0) REVERT: B 188 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: B 193 GLN cc_start: 0.8980 (mt0) cc_final: 0.8676 (mt0) REVERT: B 210 ASP cc_start: 0.7830 (t70) cc_final: 0.7478 (t0) REVERT: B 242 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7697 (tm-30) REVERT: B 243 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7519 (mtt) REVERT: C 185 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: C 210 ASP cc_start: 0.7851 (t70) cc_final: 0.7284 (t70) REVERT: C 279 MET cc_start: 0.8773 (tpp) cc_final: 0.8507 (mmm) REVERT: C 287 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7650 (tpp80) REVERT: C 337 ARG cc_start: 0.6314 (mmm160) cc_final: 0.4990 (mtp180) REVERT: C 363 LEU cc_start: 0.7573 (tp) cc_final: 0.7251 (mp) REVERT: D 96 ASP cc_start: 0.6784 (p0) cc_final: 0.6390 (p0) REVERT: D 159 LYS cc_start: 0.8681 (tmmt) cc_final: 0.8216 (mttm) REVERT: D 166 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: D 173 GLU cc_start: 0.8291 (tt0) cc_final: 0.7989 (tt0) REVERT: D 185 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: D 193 GLN cc_start: 0.8887 (mt0) cc_final: 0.8619 (mt0) REVERT: D 242 GLN cc_start: 0.8149 (tp-100) cc_final: 0.7657 (tm-30) REVERT: D 314 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7219 (tt) outliers start: 40 outliers final: 25 residues processed: 223 average time/residue: 0.5786 time to fit residues: 141.8586 Evaluate side-chains 210 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 314 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 142 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 168 optimal weight: 0.1980 chunk 74 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 166 optimal weight: 0.0370 chunk 115 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 ASN A 82 GLN C 282 GLN D 82 GLN D 282 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.132261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102749 restraints weight = 64486.440| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.96 r_work: 0.3011 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14265 Z= 0.130 Angle : 0.669 12.690 19395 Z= 0.331 Chirality : 0.045 0.261 2205 Planarity : 0.004 0.047 2410 Dihedral : 5.691 52.093 2075 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.25 % Allowed : 15.96 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.03 (0.21), residues: 1705 helix: 2.13 (0.23), residues: 555 sheet: -0.60 (0.26), residues: 385 loop : -1.25 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 287 TYR 0.020 0.001 TYR E 317 PHE 0.025 0.001 PHE C 356 TRP 0.011 0.001 TRP A 358 HIS 0.001 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00293 (14245) covalent geometry : angle 0.62702 (19345) SS BOND : bond 0.00634 ( 10) SS BOND : angle 4.83841 ( 20) hydrogen bonds : bond 0.03374 ( 660) hydrogen bonds : angle 4.64097 ( 2335) link_BETA1-4 : bond 0.00362 ( 5) link_BETA1-4 : angle 1.22060 ( 15) link_NAG-ASN : bond 0.01619 ( 5) link_NAG-ASN : angle 6.21997 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: E 100 ASP cc_start: 0.8360 (p0) cc_final: 0.7708 (m-30) REVERT: E 159 LYS cc_start: 0.8719 (tmmt) cc_final: 0.8496 (tttp) REVERT: E 189 LYS cc_start: 0.8457 (tptp) cc_final: 0.8171 (tppp) REVERT: E 214 CYS cc_start: 0.6813 (p) cc_final: 0.6552 (p) REVERT: E 242 GLN cc_start: 0.8256 (tp-100) cc_final: 0.7817 (tm-30) REVERT: E 253 LEU cc_start: 0.8589 (mt) cc_final: 0.8229 (mt) REVERT: E 262 MET cc_start: 0.5211 (mpt) cc_final: 0.4951 (mpt) REVERT: E 337 ARG cc_start: 0.6372 (tpp80) cc_final: 0.5286 (mtt180) REVERT: E 339 ASP cc_start: 0.6382 (t0) cc_final: 0.5970 (t0) REVERT: E 363 LEU cc_start: 0.7533 (tp) cc_final: 0.7247 (mp) REVERT: A 105 MET cc_start: 0.8308 (mmm) cc_final: 0.7929 (mmm) REVERT: A 159 LYS cc_start: 0.8681 (tmmt) cc_final: 0.8115 (mttm) REVERT: A 185 GLU cc_start: 0.8380 (pt0) cc_final: 0.8089 (mt-10) REVERT: A 193 GLN cc_start: 0.8910 (mt0) cc_final: 0.8559 (mt0) REVERT: A 361 TYR cc_start: 0.8520 (m-80) cc_final: 0.8012 (m-80) REVERT: B 96 ASP cc_start: 0.6214 (p0) cc_final: 0.5463 (p0) REVERT: B 188 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: B 193 GLN cc_start: 0.8975 (mt0) cc_final: 0.8674 (mt0) REVERT: B 210 ASP cc_start: 0.7828 (t70) cc_final: 0.7527 (t70) REVERT: B 242 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7679 (tm-30) REVERT: B 243 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7564 (mtt) REVERT: C 210 ASP cc_start: 0.7897 (t70) cc_final: 0.7381 (t70) REVERT: C 279 MET cc_start: 0.8775 (tpp) cc_final: 0.8517 (mmm) REVERT: C 300 ASP cc_start: 0.8589 (m-30) cc_final: 0.8345 (m-30) REVERT: C 337 ARG cc_start: 0.6330 (mmm160) cc_final: 0.4993 (mtp180) REVERT: C 363 LEU cc_start: 0.7566 (tp) cc_final: 0.7315 (mp) REVERT: D 159 LYS cc_start: 0.8687 (tmmt) cc_final: 0.8224 (mttm) REVERT: D 166 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: D 173 GLU cc_start: 0.8271 (tt0) cc_final: 0.7978 (tt0) REVERT: D 185 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: D 193 GLN cc_start: 0.8878 (mt0) cc_final: 0.8608 (mt0) REVERT: D 314 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7092 (tt) outliers start: 34 outliers final: 23 residues processed: 214 average time/residue: 0.5116 time to fit residues: 121.2658 Evaluate side-chains 210 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 314 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 43 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 0.0870 chunk 149 optimal weight: 0.6980 chunk 160 optimal weight: 0.0010 chunk 8 optimal weight: 0.0010 chunk 39 optimal weight: 0.9990 overall best weight: 0.2770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN A 242 GLN B 82 GLN C 82 GLN C 242 GLN C 282 GLN D 282 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.104730 restraints weight = 62743.798| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.95 r_work: 0.3056 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14265 Z= 0.115 Angle : 0.645 12.291 19395 Z= 0.321 Chirality : 0.044 0.267 2205 Planarity : 0.004 0.044 2410 Dihedral : 5.518 51.072 2075 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.25 % Allowed : 16.36 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.10 (0.21), residues: 1705 helix: 2.24 (0.23), residues: 555 sheet: -0.54 (0.26), residues: 385 loop : -1.26 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 287 TYR 0.016 0.001 TYR E 317 PHE 0.025 0.001 PHE C 356 TRP 0.017 0.001 TRP E 358 HIS 0.001 0.000 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00252 (14245) covalent geometry : angle 0.60448 (19345) SS BOND : bond 0.00529 ( 10) SS BOND : angle 4.43246 ( 20) hydrogen bonds : bond 0.03258 ( 660) hydrogen bonds : angle 4.50783 ( 2335) link_BETA1-4 : bond 0.00409 ( 5) link_BETA1-4 : angle 1.28177 ( 15) link_NAG-ASN : bond 0.01617 ( 5) link_NAG-ASN : angle 6.24498 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: E 100 ASP cc_start: 0.8287 (p0) cc_final: 0.7730 (m-30) REVERT: E 159 LYS cc_start: 0.8727 (tmmt) cc_final: 0.8172 (mttt) REVERT: E 210 ASP cc_start: 0.7710 (t70) cc_final: 0.7018 (t70) REVERT: E 214 CYS cc_start: 0.6734 (p) cc_final: 0.6474 (p) REVERT: E 242 GLN cc_start: 0.8203 (tp-100) cc_final: 0.7729 (tm-30) REVERT: E 253 LEU cc_start: 0.8568 (mt) cc_final: 0.8176 (mt) REVERT: E 337 ARG cc_start: 0.6371 (tpp80) cc_final: 0.5344 (mtt180) REVERT: E 339 ASP cc_start: 0.6294 (t0) cc_final: 0.5942 (t0) REVERT: E 363 LEU cc_start: 0.7534 (tp) cc_final: 0.7260 (mp) REVERT: A 105 MET cc_start: 0.8326 (mmm) cc_final: 0.7970 (mmm) REVERT: A 159 LYS cc_start: 0.8689 (tmmt) cc_final: 0.8165 (mttm) REVERT: A 185 GLU cc_start: 0.8289 (pt0) cc_final: 0.8086 (mt-10) REVERT: A 193 GLN cc_start: 0.8936 (mt0) cc_final: 0.8581 (mt0) REVERT: B 96 ASP cc_start: 0.6168 (p0) cc_final: 0.5262 (p0) REVERT: B 188 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: B 193 GLN cc_start: 0.8968 (mt0) cc_final: 0.8663 (mt0) REVERT: B 210 ASP cc_start: 0.7775 (t70) cc_final: 0.7448 (t70) REVERT: B 242 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7715 (tm-30) REVERT: B 243 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7534 (mtt) REVERT: C 159 LYS cc_start: 0.8697 (tmmt) cc_final: 0.8254 (mttm) REVERT: C 185 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7338 (mm-30) REVERT: C 210 ASP cc_start: 0.7878 (t70) cc_final: 0.7351 (t70) REVERT: C 279 MET cc_start: 0.8776 (tpp) cc_final: 0.8553 (tpt) REVERT: C 287 ARG cc_start: 0.7788 (tpp80) cc_final: 0.7184 (mtm-85) REVERT: C 300 ASP cc_start: 0.8627 (m-30) cc_final: 0.8380 (m-30) REVERT: C 337 ARG cc_start: 0.6327 (mmm160) cc_final: 0.4992 (mtp180) REVERT: C 363 LEU cc_start: 0.7584 (tp) cc_final: 0.7380 (mp) REVERT: D 96 ASP cc_start: 0.6054 (p0) cc_final: 0.3889 (t70) REVERT: D 159 LYS cc_start: 0.8731 (tmmt) cc_final: 0.8179 (mttt) REVERT: D 166 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7150 (mp10) REVERT: D 173 GLU cc_start: 0.8228 (tt0) cc_final: 0.7903 (tt0) REVERT: D 193 GLN cc_start: 0.8867 (mt0) cc_final: 0.8598 (mt0) outliers start: 34 outliers final: 24 residues processed: 223 average time/residue: 0.4922 time to fit residues: 122.0116 Evaluate side-chains 205 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 70 optimal weight: 0.7980 chunk 126 optimal weight: 0.0970 chunk 80 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 ASN E 82 GLN A 82 GLN A 242 GLN B 82 GLN C 82 GLN C 242 GLN C 282 GLN D 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100734 restraints weight = 72276.959| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 4.18 r_work: 0.2987 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14265 Z= 0.157 Angle : 0.684 13.123 19395 Z= 0.341 Chirality : 0.046 0.257 2205 Planarity : 0.004 0.045 2410 Dihedral : 5.604 49.777 2075 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.72 % Allowed : 16.36 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.14 (0.21), residues: 1705 helix: 2.32 (0.23), residues: 545 sheet: -0.58 (0.26), residues: 385 loop : -1.20 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 287 TYR 0.015 0.002 TYR E 144 PHE 0.026 0.002 PHE C 356 TRP 0.018 0.002 TRP E 358 HIS 0.003 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00361 (14245) covalent geometry : angle 0.64416 (19345) SS BOND : bond 0.00693 ( 10) SS BOND : angle 4.81838 ( 20) hydrogen bonds : bond 0.03428 ( 660) hydrogen bonds : angle 4.61796 ( 2335) link_BETA1-4 : bond 0.00373 ( 5) link_BETA1-4 : angle 1.03703 ( 15) link_NAG-ASN : bond 0.01616 ( 5) link_NAG-ASN : angle 6.16926 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 100 ASP cc_start: 0.8367 (p0) cc_final: 0.7764 (m-30) REVERT: E 159 LYS cc_start: 0.8783 (tmmt) cc_final: 0.8569 (tttp) REVERT: E 189 LYS cc_start: 0.8477 (tptp) cc_final: 0.8192 (tppp) REVERT: E 210 ASP cc_start: 0.7797 (t70) cc_final: 0.7081 (t70) REVERT: E 214 CYS cc_start: 0.6866 (p) cc_final: 0.6625 (p) REVERT: E 253 LEU cc_start: 0.8595 (mt) cc_final: 0.8179 (mt) REVERT: E 262 MET cc_start: 0.5093 (mpt) cc_final: 0.4842 (mpt) REVERT: E 314 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.8001 (tt) REVERT: E 337 ARG cc_start: 0.6392 (tpp80) cc_final: 0.5288 (mtp-110) REVERT: E 339 ASP cc_start: 0.6446 (t0) cc_final: 0.6086 (t0) REVERT: E 363 LEU cc_start: 0.7536 (tp) cc_final: 0.7283 (mp) REVERT: A 105 MET cc_start: 0.8308 (mmm) cc_final: 0.7947 (mmm) REVERT: A 159 LYS cc_start: 0.8680 (tmmt) cc_final: 0.8129 (mttm) REVERT: A 166 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: A 185 GLU cc_start: 0.8369 (pt0) cc_final: 0.8115 (mt-10) REVERT: A 193 GLN cc_start: 0.8911 (mt0) cc_final: 0.8557 (mt0) REVERT: B 96 ASP cc_start: 0.6314 (p0) cc_final: 0.5656 (p0) REVERT: B 188 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: B 193 GLN cc_start: 0.8998 (mt0) cc_final: 0.8665 (mt0) REVERT: B 210 ASP cc_start: 0.7847 (t70) cc_final: 0.7532 (t70) REVERT: B 242 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7611 (tm-30) REVERT: B 243 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7647 (mtt) REVERT: C 185 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7398 (mm-30) REVERT: C 210 ASP cc_start: 0.7862 (t70) cc_final: 0.7336 (t70) REVERT: C 279 MET cc_start: 0.8818 (tpp) cc_final: 0.8514 (mmm) REVERT: C 287 ARG cc_start: 0.7809 (tpp80) cc_final: 0.7298 (mtt180) REVERT: C 337 ARG cc_start: 0.6340 (mmm160) cc_final: 0.5045 (mtp-110) REVERT: C 363 LEU cc_start: 0.7563 (tp) cc_final: 0.7323 (mp) REVERT: D 96 ASP cc_start: 0.6407 (p0) cc_final: 0.5575 (p0) REVERT: D 173 GLU cc_start: 0.8292 (tt0) cc_final: 0.8014 (tt0) REVERT: D 185 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: D 193 GLN cc_start: 0.8890 (mt0) cc_final: 0.8618 (mt0) REVERT: D 337 ARG cc_start: 0.6384 (mmm160) cc_final: 0.5072 (mtp180) outliers start: 41 outliers final: 29 residues processed: 210 average time/residue: 0.5464 time to fit residues: 126.5555 Evaluate side-chains 210 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 314 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 47 ASN C 242 GLN C 282 GLN D 139 ASN D 282 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.098997 restraints weight = 61236.396| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.90 r_work: 0.2982 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.004 0.055 14265 Z= 0.162 Angle : 0.695 13.021 19395 Z= 0.346 Chirality : 0.046 0.257 2205 Planarity : 0.004 0.052 2410 Dihedral : 5.607 50.177 2075 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.45 % Allowed : 17.22 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.10 (0.21), residues: 1705 helix: 2.20 (0.23), residues: 560 sheet: -0.59 (0.26), residues: 385 loop : -1.24 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 287 TYR 0.015 0.002 TYR C 144 PHE 0.027 0.002 PHE C 356 TRP 0.017 0.001 TRP A 358 HIS 0.002 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00377 (14245) covalent geometry : angle 0.65501 (19345) SS BOND : bond 0.00675 ( 10) SS BOND : angle 4.90973 ( 20) hydrogen bonds : bond 0.03457 ( 660) hydrogen bonds : angle 4.62051 ( 2335) link_BETA1-4 : bond 0.00360 ( 5) link_BETA1-4 : angle 1.08993 ( 15) link_NAG-ASN : bond 0.01630 ( 5) link_NAG-ASN : angle 6.22912 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: E 100 ASP cc_start: 0.8309 (p0) cc_final: 0.7749 (m-30) REVERT: E 159 LYS cc_start: 0.8787 (tmmt) cc_final: 0.8539 (tttp) REVERT: E 189 LYS cc_start: 0.8455 (tptp) cc_final: 0.8155 (tppp) REVERT: E 214 CYS cc_start: 0.6906 (p) cc_final: 0.6644 (p) REVERT: E 253 LEU cc_start: 0.8585 (mt) cc_final: 0.8167 (mt) REVERT: E 262 MET cc_start: 0.5121 (mpt) cc_final: 0.4899 (mpt) REVERT: E 337 ARG cc_start: 0.6436 (tpp80) cc_final: 0.5406 (mtp180) REVERT: E 339 ASP cc_start: 0.6474 (t0) cc_final: 0.6132 (t0) REVERT: E 363 LEU cc_start: 0.7490 (tp) cc_final: 0.7262 (mp) REVERT: A 105 MET cc_start: 0.8300 (mmm) cc_final: 0.7936 (mmm) REVERT: A 159 LYS cc_start: 0.8686 (tmmt) cc_final: 0.8069 (mttm) REVERT: A 166 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.7184 (mp10) REVERT: A 185 GLU cc_start: 0.8356 (pt0) cc_final: 0.8092 (mt-10) REVERT: A 193 GLN cc_start: 0.8894 (mt0) cc_final: 0.8536 (mt0) REVERT: B 96 ASP cc_start: 0.6300 (p0) cc_final: 0.5415 (p0) REVERT: B 188 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: B 193 GLN cc_start: 0.8993 (mt0) cc_final: 0.8662 (mt0) REVERT: B 210 ASP cc_start: 0.7877 (t70) cc_final: 0.7538 (t70) REVERT: B 242 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7659 (tm-30) REVERT: B 243 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7593 (mtt) REVERT: C 185 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: C 210 ASP cc_start: 0.7838 (t70) cc_final: 0.7320 (t70) REVERT: C 279 MET cc_start: 0.8791 (tpp) cc_final: 0.8485 (mmm) REVERT: C 287 ARG cc_start: 0.7796 (tpp80) cc_final: 0.7306 (mtm-85) REVERT: C 300 ASP cc_start: 0.8602 (m-30) cc_final: 0.8402 (m-30) REVERT: C 337 ARG cc_start: 0.6320 (mmm160) cc_final: 0.4991 (mtp180) REVERT: C 363 LEU cc_start: 0.7578 (tp) cc_final: 0.7335 (mp) REVERT: D 96 ASP cc_start: 0.6383 (p0) cc_final: 0.5531 (p0) REVERT: D 173 GLU cc_start: 0.8279 (tt0) cc_final: 0.7967 (tt0) REVERT: D 185 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: D 193 GLN cc_start: 0.8856 (mt0) cc_final: 0.8553 (mt0) outliers start: 37 outliers final: 29 residues processed: 196 average time/residue: 0.5456 time to fit residues: 117.9454 Evaluate side-chains 205 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.0270 chunk 161 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 138 optimal weight: 0.0670 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN C 282 GLN D 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.102708 restraints weight = 65315.323| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 4.07 r_work: 0.3028 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14265 Z= 0.124 Angle : 0.652 12.458 19395 Z= 0.325 Chirality : 0.045 0.264 2205 Planarity : 0.004 0.050 2410 Dihedral : 5.416 50.490 2075 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.12 % Allowed : 18.01 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.12 (0.21), residues: 1705 helix: 2.22 (0.23), residues: 565 sheet: -0.60 (0.26), residues: 385 loop : -1.22 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 287 TYR 0.011 0.001 TYR E 144 PHE 0.027 0.001 PHE C 356 TRP 0.012 0.001 TRP D 358 HIS 0.001 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00276 (14245) covalent geometry : angle 0.61143 (19345) SS BOND : bond 0.00572 ( 10) SS BOND : angle 4.44667 ( 20) hydrogen bonds : bond 0.03279 ( 660) hydrogen bonds : angle 4.49557 ( 2335) link_BETA1-4 : bond 0.00492 ( 5) link_BETA1-4 : angle 1.27546 ( 15) link_NAG-ASN : bond 0.01650 ( 5) link_NAG-ASN : angle 6.24510 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: E 100 ASP cc_start: 0.8247 (p0) cc_final: 0.7785 (m-30) REVERT: E 159 LYS cc_start: 0.8788 (tmmt) cc_final: 0.8554 (tttp) REVERT: E 210 ASP cc_start: 0.7885 (t70) cc_final: 0.7223 (t70) REVERT: E 214 CYS cc_start: 0.6826 (p) cc_final: 0.6584 (p) REVERT: E 253 LEU cc_start: 0.8576 (mt) cc_final: 0.8164 (mt) REVERT: E 337 ARG cc_start: 0.6472 (tpp80) cc_final: 0.5479 (mtp180) REVERT: E 339 ASP cc_start: 0.6411 (t0) cc_final: 0.6128 (t0) REVERT: A 105 MET cc_start: 0.8354 (mmm) cc_final: 0.7980 (mmm) REVERT: A 159 LYS cc_start: 0.8701 (tmmt) cc_final: 0.8162 (mttm) REVERT: A 166 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.7033 (mp10) REVERT: A 185 GLU cc_start: 0.8367 (pt0) cc_final: 0.8124 (mt-10) REVERT: A 193 GLN cc_start: 0.8895 (mt0) cc_final: 0.8538 (mt0) REVERT: B 96 ASP cc_start: 0.6234 (p0) cc_final: 0.5608 (p0) REVERT: B 188 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: B 193 GLN cc_start: 0.8989 (mt0) cc_final: 0.8661 (mt0) REVERT: B 210 ASP cc_start: 0.7823 (t70) cc_final: 0.7477 (t70) REVERT: B 242 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7638 (tm-30) REVERT: B 243 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7540 (mtt) REVERT: C 159 LYS cc_start: 0.8728 (tmmt) cc_final: 0.8290 (mttm) REVERT: C 185 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7358 (mm-30) REVERT: C 210 ASP cc_start: 0.7880 (t70) cc_final: 0.7404 (t70) REVERT: C 279 MET cc_start: 0.8803 (tpp) cc_final: 0.8585 (tpt) REVERT: C 287 ARG cc_start: 0.7807 (tpp80) cc_final: 0.7306 (mtt180) REVERT: C 300 ASP cc_start: 0.8607 (m-30) cc_final: 0.8400 (m-30) REVERT: C 337 ARG cc_start: 0.6417 (mmm160) cc_final: 0.5061 (mtp180) REVERT: C 363 LEU cc_start: 0.7615 (tp) cc_final: 0.7399 (mp) REVERT: D 96 ASP cc_start: 0.6262 (p0) cc_final: 0.5372 (p0) REVERT: D 185 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: D 193 GLN cc_start: 0.8884 (mt0) cc_final: 0.8585 (mt0) outliers start: 32 outliers final: 26 residues processed: 198 average time/residue: 0.5492 time to fit residues: 119.9813 Evaluate side-chains 198 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 61 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 106 optimal weight: 0.0770 chunk 43 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 47 ASN C 139 ASN C 282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098777 restraints weight = 69048.250| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 4.12 r_work: 0.2983 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14265 Z= 0.153 Angle : 0.685 12.889 19395 Z= 0.342 Chirality : 0.046 0.258 2205 Planarity : 0.004 0.051 2410 Dihedral : 5.450 49.792 2075 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.52 % Allowed : 18.15 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.12 (0.21), residues: 1705 helix: 2.18 (0.23), residues: 565 sheet: -0.63 (0.26), residues: 385 loop : -1.18 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 287 TYR 0.014 0.002 TYR E 144 PHE 0.027 0.002 PHE C 356 TRP 0.013 0.001 TRP D 358 HIS 0.002 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00353 (14245) covalent geometry : angle 0.64479 (19345) SS BOND : bond 0.00653 ( 10) SS BOND : angle 4.83274 ( 20) hydrogen bonds : bond 0.03385 ( 660) hydrogen bonds : angle 4.54843 ( 2335) link_BETA1-4 : bond 0.00369 ( 5) link_BETA1-4 : angle 1.06821 ( 15) link_NAG-ASN : bond 0.01610 ( 5) link_NAG-ASN : angle 6.20908 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4592.79 seconds wall clock time: 78 minutes 59.45 seconds (4739.45 seconds total)