Starting phenix.real_space_refine on Sun Jan 19 01:22:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.map" model { file = "/net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 8485 2.51 5 N 2190 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13070 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2572 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306} Chain breaks: 1 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2572 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306} Chain breaks: 1 Chain: "C" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2572 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306} Chain breaks: 1 Chain: "D" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2572 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306} Chain breaks: 1 Chain: "E" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2572 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306} Chain breaks: 1 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" C1 NAG F 2 " occ=0.60 ... (12 atoms not shown) pdb=" O7 NAG F 2 " occ=0.60 residue: pdb=" C1 NAG G 2 " occ=0.60 ... (12 atoms not shown) pdb=" O7 NAG G 2 " occ=0.60 residue: pdb=" C1 NAG H 2 " occ=0.60 ... (12 atoms not shown) pdb=" O7 NAG H 2 " occ=0.60 residue: pdb=" C1 NAG I 2 " occ=0.60 ... (12 atoms not shown) pdb=" O7 NAG I 2 " occ=0.60 residue: pdb=" C1 NAG J 2 " occ=0.60 ... (12 atoms not shown) pdb=" O7 NAG J 2 " occ=0.60 Time building chain proxies: 7.81, per 1000 atoms: 0.60 Number of scatterers: 13070 At special positions: 0 Unit cell: (93, 93, 121.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 2340 8.00 N 2190 7.00 C 8485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 394 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 289 " - pdb=" SG CYS D 394 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 394 " distance=2.03 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 A 501 " - " ASN A 170 " " NAG B 501 " - " ASN B 170 " " NAG C 501 " - " ASN C 170 " " NAG D 501 " - " ASN D 170 " " NAG E 501 " - " ASN E 170 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN B 55 " " NAG H 1 " - " ASN C 55 " " NAG I 1 " - " ASN D 55 " " NAG J 1 " - " ASN E 55 " Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.7 seconds 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3140 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 36.7% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.465A pdb=" N VAL A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 259 through 283 removed outlier: 4.175A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 320 removed outlier: 3.998A pdb=" N TYR A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 392 Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 231 through 252 removed outlier: 4.463A pdb=" N VAL B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 259 through 283 removed outlier: 4.175A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 320 removed outlier: 3.998A pdb=" N TYR B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 392 Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 231 through 252 removed outlier: 4.463A pdb=" N VAL C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 259 through 283 removed outlier: 4.175A pdb=" N GLY C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 320 removed outlier: 3.998A pdb=" N TYR C 295 " --> pdb=" O PRO C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 392 Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 231 through 252 removed outlier: 4.465A pdb=" N VAL D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Proline residue: D 240 - end of helix Processing helix chain 'D' and resid 259 through 283 removed outlier: 4.175A pdb=" N GLY D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 320 removed outlier: 3.998A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 392 Processing helix chain 'D' and resid 399 through 404 Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 231 through 252 removed outlier: 4.464A pdb=" N VAL E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) Proline residue: E 240 - end of helix Processing helix chain 'E' and resid 259 through 283 removed outlier: 4.175A pdb=" N GLY E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 320 removed outlier: 3.998A pdb=" N TYR E 295 " --> pdb=" O PRO E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 392 Processing helix chain 'E' and resid 399 through 404 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 5.688A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ALA A 150 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TRP A 130 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA A 152 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 128 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU A 154 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 5.688A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN A 73 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET A 84 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL A 71 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LEU A 86 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER A 69 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ARG A 88 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE A 67 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER A 90 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG A 65 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU A 92 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N ASP A 63 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 122 removed outlier: 4.115A pdb=" N ASP A 206 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS A 227 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL A 204 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 5.687A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA B 150 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP B 130 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA B 152 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B 128 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU B 154 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111 removed outlier: 5.687A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN B 73 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET B 84 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL B 71 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N LEU B 86 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER B 69 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ARG B 88 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE B 67 " --> pdb=" O ARG B 88 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER B 90 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ARG B 65 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU B 92 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N ASP B 63 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 122 removed outlier: 4.115A pdb=" N ASP B 206 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS B 227 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL B 204 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111 removed outlier: 5.687A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ALA C 150 " --> pdb=" O TRP C 130 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TRP C 130 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA C 152 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL C 128 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU C 154 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 111 removed outlier: 5.687A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN C 73 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET C 84 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL C 71 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LEU C 86 " --> pdb=" O SER C 69 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER C 69 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ARG C 88 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE C 67 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER C 90 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ARG C 65 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU C 92 " --> pdb=" O ASP C 63 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N ASP C 63 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.114A pdb=" N ASP C 206 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS C 227 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL C 204 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111 removed outlier: 5.688A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA D 150 " --> pdb=" O TRP D 130 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP D 130 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA D 152 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL D 128 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU D 154 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 111 removed outlier: 5.688A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN D 73 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET D 84 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL D 71 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N LEU D 86 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER D 69 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ARG D 88 " --> pdb=" O PHE D 67 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE D 67 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER D 90 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG D 65 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU D 92 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N ASP D 63 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 121 through 122 removed outlier: 4.115A pdb=" N ASP D 206 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS D 227 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL D 204 " --> pdb=" O LYS D 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111 removed outlier: 5.687A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA E 150 " --> pdb=" O TRP E 130 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TRP E 130 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA E 152 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL E 128 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU E 154 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 111 removed outlier: 5.687A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN E 73 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N MET E 84 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL E 71 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LEU E 86 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER E 69 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ARG E 88 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE E 67 " --> pdb=" O ARG E 88 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER E 90 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG E 65 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU E 92 " --> pdb=" O ASP E 63 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N ASP E 63 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 121 through 122 removed outlier: 4.114A pdb=" N ASP E 206 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS E 227 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL E 204 " --> pdb=" O LYS E 227 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2100 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.13 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2020 1.31 - 1.44: 3605 1.44 - 1.56: 7685 1.56 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 13385 Sorted by residual: bond pdb=" C7 NAG J 1 " pdb=" N2 NAG J 1 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C7 NAG H 2 " pdb=" N2 NAG H 2 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C7 NAG H 1 " pdb=" N2 NAG H 1 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C7 NAG J 2 " pdb=" N2 NAG J 2 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C7 NAG F 2 " pdb=" N2 NAG F 2 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.39e+01 ... (remaining 13380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 17547 1.10 - 2.20: 461 2.20 - 3.30: 169 3.30 - 4.40: 81 4.40 - 5.50: 47 Bond angle restraints: 18305 Sorted by residual: angle pdb=" C4 NAG H 2 " pdb=" C5 NAG H 2 " pdb=" C6 NAG H 2 " ideal model delta sigma weight residual 113.89 108.79 5.10 3.00e+00 1.11e-01 2.89e+00 angle pdb=" C4 NAG G 2 " pdb=" C5 NAG G 2 " pdb=" C6 NAG G 2 " ideal model delta sigma weight residual 113.89 108.81 5.08 3.00e+00 1.11e-01 2.87e+00 angle pdb=" C4 NAG F 2 " pdb=" C5 NAG F 2 " pdb=" C6 NAG F 2 " ideal model delta sigma weight residual 113.89 108.81 5.08 3.00e+00 1.11e-01 2.87e+00 angle pdb=" C4 NAG I 2 " pdb=" C5 NAG I 2 " pdb=" C6 NAG I 2 " ideal model delta sigma weight residual 113.89 108.82 5.07 3.00e+00 1.11e-01 2.86e+00 angle pdb=" C4 NAG J 2 " pdb=" C5 NAG J 2 " pdb=" C6 NAG J 2 " ideal model delta sigma weight residual 113.89 108.84 5.05 3.00e+00 1.11e-01 2.84e+00 ... (remaining 18300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7582 17.97 - 35.94: 523 35.94 - 53.91: 60 53.91 - 71.87: 5 71.87 - 89.84: 10 Dihedral angle restraints: 8180 sinusoidal: 3385 harmonic: 4795 Sorted by residual: dihedral pdb=" CA VAL B 71 " pdb=" C VAL B 71 " pdb=" N PHE B 72 " pdb=" CA PHE B 72 " ideal model delta harmonic sigma weight residual -180.00 -165.58 -14.42 0 5.00e+00 4.00e-02 8.31e+00 dihedral pdb=" CA VAL D 71 " pdb=" C VAL D 71 " pdb=" N PHE D 72 " pdb=" CA PHE D 72 " ideal model delta harmonic sigma weight residual -180.00 -165.60 -14.40 0 5.00e+00 4.00e-02 8.29e+00 dihedral pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" N PHE A 72 " pdb=" CA PHE A 72 " ideal model delta harmonic sigma weight residual 180.00 -165.62 -14.38 0 5.00e+00 4.00e-02 8.27e+00 ... (remaining 8177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1462 0.031 - 0.063: 539 0.063 - 0.094: 129 0.094 - 0.126: 80 0.126 - 0.157: 25 Chirality restraints: 2235 Sorted by residual: chirality pdb=" CA PHE A 72 " pdb=" N PHE A 72 " pdb=" C PHE A 72 " pdb=" CB PHE A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA PHE E 72 " pdb=" N PHE E 72 " pdb=" C PHE E 72 " pdb=" CB PHE E 72 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA PHE B 72 " pdb=" N PHE B 72 " pdb=" C PHE B 72 " pdb=" CB PHE B 72 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 2232 not shown) Planarity restraints: 2260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 72 " -0.010 2.00e-02 2.50e+03 8.91e-03 1.39e+00 pdb=" CG PHE B 72 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE B 72 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 72 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 72 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 72 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 72 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 72 " 0.010 2.00e-02 2.50e+03 8.88e-03 1.38e+00 pdb=" CG PHE C 72 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE C 72 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 72 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 72 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 72 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 72 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 72 " 0.010 2.00e-02 2.50e+03 8.72e-03 1.33e+00 pdb=" CG PHE D 72 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 72 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 72 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 72 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 72 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 72 " 0.003 2.00e-02 2.50e+03 ... (remaining 2257 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2871 2.80 - 3.33: 11982 3.33 - 3.85: 22222 3.85 - 4.38: 25474 4.38 - 4.90: 44314 Nonbonded interactions: 106863 Sorted by model distance: nonbonded pdb=" OE2 GLU D 242 " pdb=" OH TYR D 296 " model vdw 2.281 3.040 nonbonded pdb=" OE2 GLU B 242 " pdb=" OH TYR B 296 " model vdw 2.281 3.040 nonbonded pdb=" OE2 GLU A 242 " pdb=" OH TYR A 296 " model vdw 2.281 3.040 nonbonded pdb=" OE2 GLU C 242 " pdb=" OH TYR C 296 " model vdw 2.281 3.040 nonbonded pdb=" NE1 TRP B 127 " pdb=" OE1 GLU B 154 " model vdw 2.282 3.120 ... (remaining 106858 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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=0.60 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 30.690 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 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 0.117 13385 Z= 0.429 Angle : 0.578 5.495 18305 Z= 0.265 Chirality : 0.040 0.157 2235 Planarity : 0.003 0.029 2250 Dihedral : 12.018 89.842 5010 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.21), residues: 1600 helix: 3.04 (0.20), residues: 530 sheet: 1.44 (0.25), residues: 495 loop : 0.04 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 91 HIS 0.001 0.000 HIS B 276 PHE 0.021 0.001 PHE C 72 TYR 0.009 0.001 TYR A 272 ARG 0.002 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8389 (mp0) cc_final: 0.8073 (mp0) REVERT: A 176 TYR cc_start: 0.8727 (m-80) cc_final: 0.8425 (m-80) REVERT: A 184 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7873 (mt-10) REVERT: A 206 ASP cc_start: 0.8188 (t0) cc_final: 0.7831 (t0) REVERT: A 208 LYS cc_start: 0.8308 (ptpt) cc_final: 0.8039 (mtmm) REVERT: A 259 ILE cc_start: 0.9299 (pt) cc_final: 0.9050 (pp) REVERT: A 272 TYR cc_start: 0.8625 (t80) cc_final: 0.8103 (t80) REVERT: A 283 LEU cc_start: 0.8421 (mt) cc_final: 0.7824 (mp) REVERT: A 297 PHE cc_start: 0.8570 (m-80) cc_final: 0.8119 (m-80) REVERT: A 364 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7640 (mt-10) REVERT: B 75 ASP cc_start: 0.7925 (t0) cc_final: 0.7045 (t0) REVERT: B 129 ASP cc_start: 0.8050 (t0) cc_final: 0.7833 (t0) REVERT: B 206 ASP cc_start: 0.8133 (t0) cc_final: 0.7629 (t0) REVERT: B 208 LYS cc_start: 0.8348 (ptpt) cc_final: 0.8081 (mtmm) REVERT: B 259 ILE cc_start: 0.9220 (pt) cc_final: 0.8798 (pp) REVERT: B 281 GLN cc_start: 0.8557 (mm110) cc_final: 0.8330 (pt0) REVERT: B 283 LEU cc_start: 0.8378 (mt) cc_final: 0.7797 (mp) REVERT: B 310 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8341 (pp20) REVERT: B 361 SER cc_start: 0.8191 (m) cc_final: 0.7662 (p) REVERT: C 75 ASP cc_start: 0.8016 (t0) cc_final: 0.7206 (t0) REVERT: C 77 LEU cc_start: 0.9344 (mt) cc_final: 0.9128 (mm) REVERT: C 124 GLU cc_start: 0.8371 (mp0) cc_final: 0.7991 (mp0) REVERT: C 129 ASP cc_start: 0.8026 (t0) cc_final: 0.7814 (t0) REVERT: C 208 LYS cc_start: 0.8453 (ptpt) cc_final: 0.8157 (mtmm) REVERT: C 279 LEU cc_start: 0.8964 (tp) cc_final: 0.8611 (tp) REVERT: C 281 GLN cc_start: 0.8559 (mm110) cc_final: 0.8328 (tt0) REVERT: C 283 LEU cc_start: 0.8597 (mt) cc_final: 0.8058 (mp) REVERT: C 297 PHE cc_start: 0.8595 (m-80) cc_final: 0.8258 (m-10) REVERT: C 361 SER cc_start: 0.8129 (m) cc_final: 0.7926 (p) REVERT: D 75 ASP cc_start: 0.8025 (t0) cc_final: 0.7304 (t0) REVERT: D 77 LEU cc_start: 0.9336 (mt) cc_final: 0.9082 (mm) REVERT: D 124 GLU cc_start: 0.8357 (mp0) cc_final: 0.8040 (mp0) REVERT: D 206 ASP cc_start: 0.8104 (t0) cc_final: 0.7884 (t0) REVERT: D 259 ILE cc_start: 0.9437 (pt) cc_final: 0.9156 (pp) REVERT: D 272 TYR cc_start: 0.8495 (t80) cc_final: 0.7830 (t80) REVERT: D 279 LEU cc_start: 0.9006 (tp) cc_final: 0.8733 (tp) REVERT: D 283 LEU cc_start: 0.8620 (mt) cc_final: 0.8066 (mp) REVERT: D 297 PHE cc_start: 0.8572 (m-80) cc_final: 0.7882 (m-10) REVERT: E 75 ASP cc_start: 0.8068 (t0) cc_final: 0.7406 (t0) REVERT: E 77 LEU cc_start: 0.9319 (mt) cc_final: 0.9075 (mm) REVERT: E 206 ASP cc_start: 0.8133 (t0) cc_final: 0.7782 (t0) REVERT: E 208 LYS cc_start: 0.8310 (ptpt) cc_final: 0.7910 (mtmm) REVERT: E 227 LYS cc_start: 0.8278 (ptmt) cc_final: 0.8042 (ptmt) REVERT: E 272 TYR cc_start: 0.8636 (t80) cc_final: 0.8185 (t80) REVERT: E 283 LEU cc_start: 0.8482 (mt) cc_final: 0.7935 (mp) REVERT: E 297 PHE cc_start: 0.8564 (m-80) cc_final: 0.7960 (m-10) outliers start: 0 outliers final: 1 residues processed: 491 average time/residue: 1.0779 time to fit residues: 583.3206 Evaluate side-chains 353 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 352 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 142 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.0870 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 145 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 215 GLN B 221 GLN C 214 GLN C 221 GLN D 221 GLN E 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.084023 restraints weight = 20225.952| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.50 r_work: 0.2905 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13385 Z= 0.178 Angle : 0.514 7.656 18305 Z= 0.253 Chirality : 0.039 0.142 2235 Planarity : 0.004 0.031 2250 Dihedral : 5.852 59.449 2062 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 2.52 % Allowed : 14.20 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.21), residues: 1600 helix: 3.21 (0.20), residues: 530 sheet: 1.35 (0.24), residues: 465 loop : 0.10 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 91 HIS 0.002 0.000 HIS C 276 PHE 0.020 0.002 PHE A 72 TYR 0.019 0.002 TYR D 176 ARG 0.007 0.001 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 371 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8478 (tp30) cc_final: 0.8058 (mm-30) REVERT: A 75 ASP cc_start: 0.8382 (t0) cc_final: 0.8053 (t0) REVERT: A 78 ARG cc_start: 0.8789 (mtp85) cc_final: 0.8568 (mtp85) REVERT: A 160 GLU cc_start: 0.8536 (tt0) cc_final: 0.7778 (tm-30) REVERT: A 176 TYR cc_start: 0.8805 (m-80) cc_final: 0.8529 (m-80) REVERT: A 201 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8307 (mp0) REVERT: A 206 ASP cc_start: 0.8461 (t0) cc_final: 0.8088 (t0) REVERT: A 208 LYS cc_start: 0.8479 (ptpt) cc_final: 0.8247 (mtmm) REVERT: A 221 GLN cc_start: 0.8721 (tt0) cc_final: 0.8404 (tt0) REVERT: A 272 TYR cc_start: 0.8852 (t80) cc_final: 0.8319 (t80) REVERT: A 283 LEU cc_start: 0.8531 (mt) cc_final: 0.8029 (mp) REVERT: A 297 PHE cc_start: 0.8772 (m-80) cc_final: 0.8404 (m-10) REVERT: A 364 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8121 (mt-10) REVERT: B 48 GLU cc_start: 0.8539 (tp30) cc_final: 0.8234 (mm-30) REVERT: B 54 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8493 (m-40) REVERT: B 75 ASP cc_start: 0.8231 (t0) cc_final: 0.7682 (t0) REVERT: B 113 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: B 129 ASP cc_start: 0.8567 (t0) cc_final: 0.8217 (t0) REVERT: B 154 GLU cc_start: 0.8670 (tt0) cc_final: 0.8412 (tt0) REVERT: B 160 GLU cc_start: 0.8587 (tt0) cc_final: 0.7927 (tm-30) REVERT: B 201 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8242 (mp0) REVERT: B 206 ASP cc_start: 0.8360 (t0) cc_final: 0.7816 (t0) REVERT: B 259 ILE cc_start: 0.9351 (pt) cc_final: 0.9018 (mt) REVERT: B 281 GLN cc_start: 0.8720 (mm110) cc_final: 0.8286 (pt0) REVERT: B 283 LEU cc_start: 0.8450 (mt) cc_final: 0.8067 (mp) REVERT: B 310 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8660 (pp20) REVERT: C 48 GLU cc_start: 0.8383 (tp30) cc_final: 0.8098 (mm-30) REVERT: C 75 ASP cc_start: 0.8267 (t0) cc_final: 0.7707 (t0) REVERT: C 77 LEU cc_start: 0.9267 (mt) cc_final: 0.9050 (mm) REVERT: C 124 GLU cc_start: 0.8976 (mp0) cc_final: 0.8695 (mp0) REVERT: C 129 ASP cc_start: 0.8568 (t0) cc_final: 0.8236 (t0) REVERT: C 160 GLU cc_start: 0.8589 (tt0) cc_final: 0.7982 (tp30) REVERT: C 201 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8273 (mp0) REVERT: C 208 LYS cc_start: 0.8598 (ptpt) cc_final: 0.8299 (mtmm) REVERT: C 281 GLN cc_start: 0.8751 (mm110) cc_final: 0.8267 (pt0) REVERT: C 283 LEU cc_start: 0.8711 (mt) cc_final: 0.8310 (mp) REVERT: C 402 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8373 (mt-10) REVERT: D 75 ASP cc_start: 0.8394 (t0) cc_final: 0.7866 (t0) REVERT: D 77 LEU cc_start: 0.9267 (mt) cc_final: 0.9036 (mm) REVERT: D 124 GLU cc_start: 0.8847 (mp0) cc_final: 0.8342 (mp0) REVERT: D 141 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8060 (pm20) REVERT: D 160 GLU cc_start: 0.8717 (tt0) cc_final: 0.8179 (tp30) REVERT: D 188 GLN cc_start: 0.8323 (mt0) cc_final: 0.8115 (tt0) REVERT: D 201 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8346 (mp0) REVERT: D 206 ASP cc_start: 0.8376 (t0) cc_final: 0.8083 (t0) REVERT: D 208 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8441 (mtmm) REVERT: D 283 LEU cc_start: 0.8654 (mt) cc_final: 0.8235 (mp) REVERT: D 402 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8238 (mt-10) REVERT: E 75 ASP cc_start: 0.8352 (t0) cc_final: 0.7893 (t0) REVERT: E 77 LEU cc_start: 0.9219 (mt) cc_final: 0.8988 (mm) REVERT: E 78 ARG cc_start: 0.8842 (mtp85) cc_final: 0.8625 (mtm110) REVERT: E 113 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: E 160 GLU cc_start: 0.8741 (tt0) cc_final: 0.7894 (tm-30) REVERT: E 201 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8288 (mp0) REVERT: E 206 ASP cc_start: 0.8392 (t0) cc_final: 0.8027 (t0) REVERT: E 208 LYS cc_start: 0.8546 (ptpt) cc_final: 0.8190 (mtmm) REVERT: E 272 TYR cc_start: 0.8862 (t80) cc_final: 0.8362 (t80) REVERT: E 283 LEU cc_start: 0.8550 (mt) cc_final: 0.8077 (mp) REVERT: E 297 PHE cc_start: 0.8818 (m-80) cc_final: 0.8382 (m-10) REVERT: E 370 PHE cc_start: 0.8726 (t80) cc_final: 0.8500 (t80) REVERT: E 390 MET cc_start: 0.8043 (mmt) cc_final: 0.7825 (mmt) REVERT: E 402 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8247 (mt-10) outliers start: 36 outliers final: 14 residues processed: 388 average time/residue: 1.2167 time to fit residues: 516.6186 Evaluate side-chains 355 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 337 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 107 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 221 GLN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN E 156 ASN E 382 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.094348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.080267 restraints weight = 20461.817| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.79 r_work: 0.2808 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13385 Z= 0.326 Angle : 0.555 8.406 18305 Z= 0.273 Chirality : 0.041 0.217 2235 Planarity : 0.004 0.036 2250 Dihedral : 5.556 55.683 2062 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.71 % Allowed : 14.90 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.21), residues: 1600 helix: 2.85 (0.20), residues: 530 sheet: 1.28 (0.25), residues: 430 loop : -0.12 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 112 HIS 0.003 0.001 HIS E 103 PHE 0.021 0.002 PHE A 72 TYR 0.019 0.002 TYR E 176 ARG 0.007 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 346 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8375 (tp30) cc_final: 0.7938 (mm-30) REVERT: A 75 ASP cc_start: 0.8169 (t0) cc_final: 0.7777 (t0) REVERT: A 78 ARG cc_start: 0.8700 (mtp85) cc_final: 0.8454 (mtp85) REVERT: A 132 ASP cc_start: 0.8230 (m-30) cc_final: 0.7954 (t0) REVERT: A 160 GLU cc_start: 0.8403 (tt0) cc_final: 0.7553 (tm-30) REVERT: A 176 TYR cc_start: 0.8741 (m-80) cc_final: 0.8227 (m-80) REVERT: A 201 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8330 (mp0) REVERT: A 206 ASP cc_start: 0.8339 (t0) cc_final: 0.7892 (t0) REVERT: A 208 LYS cc_start: 0.8448 (ptpt) cc_final: 0.8125 (mtmm) REVERT: A 272 TYR cc_start: 0.8782 (t80) cc_final: 0.8167 (t80) REVERT: A 281 GLN cc_start: 0.8703 (mm110) cc_final: 0.8279 (pt0) REVERT: A 283 LEU cc_start: 0.8682 (mt) cc_final: 0.8270 (mp) REVERT: A 297 PHE cc_start: 0.8688 (m-80) cc_final: 0.8302 (m-10) REVERT: A 364 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7767 (mt-10) REVERT: B 75 ASP cc_start: 0.7913 (t0) cc_final: 0.7394 (t0) REVERT: B 129 ASP cc_start: 0.8529 (t0) cc_final: 0.8047 (t0) REVERT: B 146 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7639 (mttp) REVERT: B 199 LYS cc_start: 0.8185 (ptpt) cc_final: 0.7742 (ptmm) REVERT: B 201 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8163 (mp0) REVERT: B 206 ASP cc_start: 0.8288 (t0) cc_final: 0.7648 (t0) REVERT: B 208 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8149 (mtmm) REVERT: B 233 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8469 (p) REVERT: B 281 GLN cc_start: 0.8731 (mm110) cc_final: 0.8324 (pt0) REVERT: B 283 LEU cc_start: 0.8566 (mt) cc_final: 0.8155 (mp) REVERT: C 75 ASP cc_start: 0.8070 (t0) cc_final: 0.7419 (t0) REVERT: C 113 GLU cc_start: 0.8997 (mp0) cc_final: 0.8734 (mp0) REVERT: C 129 ASP cc_start: 0.8623 (t0) cc_final: 0.8180 (t0) REVERT: C 146 LYS cc_start: 0.8431 (mtpt) cc_final: 0.7741 (mtmp) REVERT: C 160 GLU cc_start: 0.8536 (tt0) cc_final: 0.7986 (mm-30) REVERT: C 184 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7907 (pt0) REVERT: C 201 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8334 (mp0) REVERT: C 208 LYS cc_start: 0.8460 (ptpt) cc_final: 0.8179 (mtmm) REVERT: C 232 LYS cc_start: 0.8623 (ttmt) cc_final: 0.8347 (ttmt) REVERT: C 233 SER cc_start: 0.8712 (m) cc_final: 0.8485 (p) REVERT: C 281 GLN cc_start: 0.8803 (mm110) cc_final: 0.8265 (pt0) REVERT: C 283 LEU cc_start: 0.8764 (mt) cc_final: 0.8376 (mp) REVERT: C 402 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8278 (mt-10) REVERT: D 48 GLU cc_start: 0.8312 (tp30) cc_final: 0.8028 (mm-30) REVERT: D 75 ASP cc_start: 0.8164 (t0) cc_final: 0.7530 (t0) REVERT: D 77 LEU cc_start: 0.9243 (mt) cc_final: 0.9004 (mm) REVERT: D 124 GLU cc_start: 0.8723 (mp0) cc_final: 0.8326 (mp0) REVERT: D 154 GLU cc_start: 0.8860 (tt0) cc_final: 0.8632 (tt0) REVERT: D 184 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7769 (pt0) REVERT: D 201 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8262 (mp0) REVERT: D 206 ASP cc_start: 0.8272 (t0) cc_final: 0.7849 (t0) REVERT: D 208 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8182 (mtmm) REVERT: D 214 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7989 (mm-40) REVERT: D 272 TYR cc_start: 0.8786 (t80) cc_final: 0.7828 (t80) REVERT: D 281 GLN cc_start: 0.8688 (mm110) cc_final: 0.8385 (mm-40) REVERT: D 283 LEU cc_start: 0.8734 (mt) cc_final: 0.8364 (mp) REVERT: D 402 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8169 (mt-10) REVERT: E 75 ASP cc_start: 0.8124 (t0) cc_final: 0.7544 (t0) REVERT: E 77 LEU cc_start: 0.9198 (mt) cc_final: 0.8915 (mm) REVERT: E 78 ARG cc_start: 0.8733 (mtp85) cc_final: 0.8487 (mtp85) REVERT: E 146 LYS cc_start: 0.8482 (mtpt) cc_final: 0.7732 (mtmp) REVERT: E 160 GLU cc_start: 0.8653 (tt0) cc_final: 0.8167 (mm-30) REVERT: E 198 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.9002 (m) REVERT: E 201 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8259 (mp0) REVERT: E 206 ASP cc_start: 0.8264 (t0) cc_final: 0.7827 (t0) REVERT: E 208 LYS cc_start: 0.8369 (ptpt) cc_final: 0.7962 (mtmm) REVERT: E 283 LEU cc_start: 0.8660 (mt) cc_final: 0.8322 (mp) outliers start: 53 outliers final: 20 residues processed: 370 average time/residue: 1.1006 time to fit residues: 449.1876 Evaluate side-chains 344 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 321 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 88 optimal weight: 3.9990 chunk 83 optimal weight: 0.0970 chunk 135 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 chunk 138 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.6356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.096203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.081618 restraints weight = 20037.920| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.89 r_work: 0.2863 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13385 Z= 0.167 Angle : 0.510 8.431 18305 Z= 0.249 Chirality : 0.039 0.180 2235 Planarity : 0.004 0.030 2250 Dihedral : 5.414 55.686 2062 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 3.15 % Allowed : 16.99 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.21), residues: 1600 helix: 2.95 (0.20), residues: 530 sheet: 0.84 (0.24), residues: 475 loop : 0.25 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 112 HIS 0.001 0.000 HIS C 276 PHE 0.017 0.002 PHE B 385 TYR 0.015 0.002 TYR E 176 ARG 0.008 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 333 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8093 (t0) cc_final: 0.7645 (t0) REVERT: A 78 ARG cc_start: 0.8573 (mtp85) cc_final: 0.8332 (mtp85) REVERT: A 141 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7927 (pm20) REVERT: A 153 THR cc_start: 0.9120 (p) cc_final: 0.8861 (t) REVERT: A 201 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8174 (mp0) REVERT: A 206 ASP cc_start: 0.8289 (t0) cc_final: 0.7850 (t0) REVERT: A 208 LYS cc_start: 0.8340 (ptpt) cc_final: 0.8034 (mtmm) REVERT: A 232 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8063 (ttmm) REVERT: A 272 TYR cc_start: 0.8686 (t80) cc_final: 0.8033 (t80) REVERT: A 281 GLN cc_start: 0.8679 (mm110) cc_final: 0.8258 (pt0) REVERT: A 283 LEU cc_start: 0.8496 (mt) cc_final: 0.8167 (mp) REVERT: A 297 PHE cc_start: 0.8544 (m-80) cc_final: 0.8136 (m-10) REVERT: A 364 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7685 (mt-10) REVERT: B 75 ASP cc_start: 0.7825 (t0) cc_final: 0.7272 (t0) REVERT: B 129 ASP cc_start: 0.8542 (t0) cc_final: 0.8027 (t0) REVERT: B 146 LYS cc_start: 0.8398 (mtmt) cc_final: 0.7583 (mttp) REVERT: B 160 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8041 (mm-30) REVERT: B 199 LYS cc_start: 0.8011 (ptpt) cc_final: 0.7762 (ptmt) REVERT: B 201 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8060 (mp0) REVERT: B 206 ASP cc_start: 0.8246 (t0) cc_final: 0.7649 (t0) REVERT: B 279 LEU cc_start: 0.8922 (tp) cc_final: 0.8690 (tt) REVERT: B 281 GLN cc_start: 0.8722 (mm110) cc_final: 0.8332 (pt0) REVERT: B 283 LEU cc_start: 0.8525 (mt) cc_final: 0.8153 (mp) REVERT: B 296 TYR cc_start: 0.8317 (t80) cc_final: 0.8076 (t80) REVERT: C 75 ASP cc_start: 0.7972 (t0) cc_final: 0.7283 (t0) REVERT: C 77 LEU cc_start: 0.9185 (mt) cc_final: 0.8949 (mm) REVERT: C 113 GLU cc_start: 0.9046 (mp0) cc_final: 0.8583 (mp0) REVERT: C 129 ASP cc_start: 0.8588 (t0) cc_final: 0.8110 (t0) REVERT: C 146 LYS cc_start: 0.8372 (mtpt) cc_final: 0.7685 (mtmp) REVERT: C 160 GLU cc_start: 0.8509 (tt0) cc_final: 0.7912 (mm-30) REVERT: C 184 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7713 (pt0) REVERT: C 201 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8262 (mp0) REVERT: C 208 LYS cc_start: 0.8372 (ptpt) cc_final: 0.8087 (mtmm) REVERT: C 232 LYS cc_start: 0.8544 (ttmt) cc_final: 0.8311 (ttmt) REVERT: C 233 SER cc_start: 0.8682 (m) cc_final: 0.8388 (p) REVERT: C 281 GLN cc_start: 0.8711 (mm110) cc_final: 0.8162 (pt0) REVERT: C 283 LEU cc_start: 0.8688 (mt) cc_final: 0.8369 (mp) REVERT: C 402 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8237 (mt-10) REVERT: D 75 ASP cc_start: 0.8090 (t0) cc_final: 0.7387 (t0) REVERT: D 77 LEU cc_start: 0.9167 (mt) cc_final: 0.8925 (mm) REVERT: D 78 ARG cc_start: 0.8763 (mtp85) cc_final: 0.8452 (mtp85) REVERT: D 160 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8318 (mm-30) REVERT: D 184 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7723 (pt0) REVERT: D 201 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8178 (mp0) REVERT: D 206 ASP cc_start: 0.8224 (t0) cc_final: 0.7821 (t0) REVERT: D 208 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8128 (mtmm) REVERT: D 281 GLN cc_start: 0.8644 (mm110) cc_final: 0.8109 (pt0) REVERT: D 283 LEU cc_start: 0.8628 (mt) cc_final: 0.8065 (mp) REVERT: D 402 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8144 (mt-10) REVERT: E 75 ASP cc_start: 0.8034 (t0) cc_final: 0.7392 (t0) REVERT: E 77 LEU cc_start: 0.9071 (mt) cc_final: 0.8836 (mm) REVERT: E 78 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8428 (mtp85) REVERT: E 113 GLU cc_start: 0.9010 (mp0) cc_final: 0.8557 (mp0) REVERT: E 146 LYS cc_start: 0.8385 (mtpt) cc_final: 0.7646 (mtmp) REVERT: E 160 GLU cc_start: 0.8621 (tt0) cc_final: 0.8125 (mm-30) REVERT: E 184 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7902 (mt-10) REVERT: E 188 GLN cc_start: 0.7994 (mt0) cc_final: 0.7683 (tt0) REVERT: E 198 VAL cc_start: 0.9255 (OUTLIER) cc_final: 0.8950 (m) REVERT: E 201 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8158 (mp0) REVERT: E 206 ASP cc_start: 0.8209 (t0) cc_final: 0.7772 (t0) REVERT: E 208 LYS cc_start: 0.8289 (ptpt) cc_final: 0.7852 (mtmm) REVERT: E 279 LEU cc_start: 0.8904 (tp) cc_final: 0.8692 (tt) REVERT: E 283 LEU cc_start: 0.8510 (mt) cc_final: 0.8060 (mp) outliers start: 45 outliers final: 20 residues processed: 356 average time/residue: 1.0504 time to fit residues: 413.7145 Evaluate side-chains 343 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 320 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 277 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 124 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN B 221 GLN C 156 ASN C 221 GLN D 156 ASN D 221 GLN D 382 GLN E 156 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.078105 restraints weight = 20677.675| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.45 r_work: 0.2793 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13385 Z= 0.265 Angle : 0.528 8.791 18305 Z= 0.257 Chirality : 0.040 0.139 2235 Planarity : 0.004 0.034 2250 Dihedral : 5.124 52.376 2060 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.36 % Allowed : 17.69 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.21), residues: 1600 helix: 2.87 (0.20), residues: 530 sheet: 0.72 (0.24), residues: 475 loop : 0.20 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 112 HIS 0.002 0.000 HIS E 103 PHE 0.019 0.002 PHE D 72 TYR 0.019 0.002 TYR D 176 ARG 0.011 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 342 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8449 (t0) cc_final: 0.8079 (t0) REVERT: A 201 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8473 (mp0) REVERT: A 206 ASP cc_start: 0.8475 (t0) cc_final: 0.8113 (t0) REVERT: A 207 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9140 (mp) REVERT: A 208 LYS cc_start: 0.8616 (ptpt) cc_final: 0.8334 (mtmm) REVERT: A 272 TYR cc_start: 0.8970 (t80) cc_final: 0.8417 (t80) REVERT: A 281 GLN cc_start: 0.8727 (mm110) cc_final: 0.8328 (pt0) REVERT: A 283 LEU cc_start: 0.8590 (mt) cc_final: 0.8254 (mp) REVERT: A 297 PHE cc_start: 0.8913 (m-80) cc_final: 0.8580 (m-10) REVERT: A 364 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8118 (mt-10) REVERT: B 75 ASP cc_start: 0.8292 (t0) cc_final: 0.7802 (t0) REVERT: B 129 ASP cc_start: 0.8824 (t0) cc_final: 0.8334 (t0) REVERT: B 146 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8092 (mttp) REVERT: B 160 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8381 (mm-30) REVERT: B 201 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8332 (mp0) REVERT: B 206 ASP cc_start: 0.8414 (t0) cc_final: 0.7918 (t0) REVERT: B 279 LEU cc_start: 0.9057 (tp) cc_final: 0.8788 (tt) REVERT: B 281 GLN cc_start: 0.8777 (mm110) cc_final: 0.8390 (pt0) REVERT: B 283 LEU cc_start: 0.8546 (mt) cc_final: 0.8209 (mp) REVERT: B 296 TYR cc_start: 0.8615 (t80) cc_final: 0.8400 (t80) REVERT: C 75 ASP cc_start: 0.8392 (t0) cc_final: 0.7790 (t0) REVERT: C 77 LEU cc_start: 0.9409 (mt) cc_final: 0.9204 (mm) REVERT: C 113 GLU cc_start: 0.9073 (mp0) cc_final: 0.8702 (mp0) REVERT: C 129 ASP cc_start: 0.8825 (t0) cc_final: 0.8350 (t0) REVERT: C 146 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8108 (mtmp) REVERT: C 160 GLU cc_start: 0.8580 (tt0) cc_final: 0.8159 (mm-30) REVERT: C 184 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8171 (pt0) REVERT: C 199 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7631 (ptmm) REVERT: C 201 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8514 (mp0) REVERT: C 233 SER cc_start: 0.8837 (m) cc_final: 0.8623 (p) REVERT: C 281 GLN cc_start: 0.8750 (mm110) cc_final: 0.8252 (pt0) REVERT: C 283 LEU cc_start: 0.8671 (mt) cc_final: 0.8359 (mp) REVERT: C 402 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8413 (mt-10) REVERT: D 48 GLU cc_start: 0.8575 (tp30) cc_final: 0.8289 (mm-30) REVERT: D 75 ASP cc_start: 0.8451 (t0) cc_final: 0.7821 (t0) REVERT: D 78 ARG cc_start: 0.8994 (mtp85) cc_final: 0.8625 (mtp85) REVERT: D 124 GLU cc_start: 0.8949 (mp0) cc_final: 0.8593 (mp0) REVERT: D 146 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8075 (mttp) REVERT: D 160 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8309 (tp30) REVERT: D 199 LYS cc_start: 0.8413 (ptpt) cc_final: 0.8142 (ptmm) REVERT: D 201 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8469 (mp0) REVERT: D 206 ASP cc_start: 0.8465 (t0) cc_final: 0.8133 (t0) REVERT: D 208 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8525 (mtmm) REVERT: D 272 TYR cc_start: 0.8952 (t80) cc_final: 0.8101 (t80) REVERT: D 281 GLN cc_start: 0.8663 (mm110) cc_final: 0.8184 (pt0) REVERT: D 283 LEU cc_start: 0.8727 (mt) cc_final: 0.8419 (mp) REVERT: D 402 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8333 (mt-10) REVERT: E 75 ASP cc_start: 0.8414 (t0) cc_final: 0.7810 (t0) REVERT: E 77 LEU cc_start: 0.9323 (mt) cc_final: 0.9106 (mm) REVERT: E 78 ARG cc_start: 0.8885 (mtp85) cc_final: 0.8680 (mtp85) REVERT: E 113 GLU cc_start: 0.9107 (mp0) cc_final: 0.8677 (mp0) REVERT: E 146 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8080 (mtmp) REVERT: E 160 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8345 (mm-30) REVERT: E 198 VAL cc_start: 0.9357 (OUTLIER) cc_final: 0.9045 (m) REVERT: E 201 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8420 (mp0) REVERT: E 206 ASP cc_start: 0.8435 (t0) cc_final: 0.8097 (t0) REVERT: E 208 LYS cc_start: 0.8610 (ptpt) cc_final: 0.8187 (mtmm) REVERT: E 279 LEU cc_start: 0.9089 (tp) cc_final: 0.8873 (tt) REVERT: E 283 LEU cc_start: 0.8649 (mt) cc_final: 0.8318 (mp) outliers start: 48 outliers final: 27 residues processed: 372 average time/residue: 1.1139 time to fit residues: 457.9235 Evaluate side-chains 364 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 331 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 379 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 107 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 221 GLN C 156 ASN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.089233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.075928 restraints weight = 20910.256| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.50 r_work: 0.2755 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13385 Z= 0.360 Angle : 0.569 8.963 18305 Z= 0.278 Chirality : 0.041 0.144 2235 Planarity : 0.004 0.033 2250 Dihedral : 5.024 48.926 2060 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.64 % Allowed : 18.53 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.21), residues: 1600 helix: 2.71 (0.20), residues: 530 sheet: 0.58 (0.24), residues: 475 loop : 0.13 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 112 HIS 0.002 0.001 HIS E 103 PHE 0.022 0.002 PHE A 72 TYR 0.021 0.002 TYR D 176 ARG 0.009 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 323 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8569 (tp30) cc_final: 0.8144 (mm-30) REVERT: A 75 ASP cc_start: 0.8393 (t0) cc_final: 0.7983 (t0) REVERT: A 132 ASP cc_start: 0.8405 (m-30) cc_final: 0.8134 (t0) REVERT: A 146 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8092 (mttp) REVERT: A 176 TYR cc_start: 0.9313 (m-80) cc_final: 0.8643 (m-80) REVERT: A 201 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8425 (mp0) REVERT: A 206 ASP cc_start: 0.8516 (t0) cc_final: 0.8148 (t0) REVERT: A 208 LYS cc_start: 0.8561 (ptpt) cc_final: 0.8246 (mtmm) REVERT: A 232 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8268 (ttmm) REVERT: A 272 TYR cc_start: 0.8959 (t80) cc_final: 0.8291 (t80) REVERT: A 281 GLN cc_start: 0.8797 (mm110) cc_final: 0.8352 (pt0) REVERT: A 283 LEU cc_start: 0.8610 (mt) cc_final: 0.8294 (mp) REVERT: A 297 PHE cc_start: 0.8877 (m-80) cc_final: 0.8506 (m-10) REVERT: A 364 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8064 (mt-10) REVERT: B 75 ASP cc_start: 0.8239 (t0) cc_final: 0.7704 (t0) REVERT: B 129 ASP cc_start: 0.8786 (t0) cc_final: 0.8258 (t0) REVERT: B 146 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8014 (mttp) REVERT: B 201 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8323 (mp0) REVERT: B 206 ASP cc_start: 0.8406 (t0) cc_final: 0.7896 (t0) REVERT: B 279 LEU cc_start: 0.9034 (tp) cc_final: 0.8765 (tt) REVERT: B 281 GLN cc_start: 0.8759 (mm110) cc_final: 0.8318 (pt0) REVERT: B 283 LEU cc_start: 0.8545 (mt) cc_final: 0.8201 (mp) REVERT: C 75 ASP cc_start: 0.8336 (t0) cc_final: 0.7722 (t0) REVERT: C 77 LEU cc_start: 0.9373 (mt) cc_final: 0.9117 (mm) REVERT: C 113 GLU cc_start: 0.9125 (mp0) cc_final: 0.8731 (mp0) REVERT: C 129 ASP cc_start: 0.8788 (t0) cc_final: 0.8253 (t0) REVERT: C 146 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8032 (mtmp) REVERT: C 160 GLU cc_start: 0.8597 (tt0) cc_final: 0.8149 (mm-30) REVERT: C 201 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8489 (mp0) REVERT: C 208 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8375 (mtmm) REVERT: C 281 GLN cc_start: 0.8763 (mm110) cc_final: 0.8278 (pt0) REVERT: C 283 LEU cc_start: 0.8670 (mt) cc_final: 0.8335 (mp) REVERT: C 402 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8387 (mt-10) REVERT: D 75 ASP cc_start: 0.8371 (t0) cc_final: 0.7746 (t0) REVERT: D 146 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7967 (mttp) REVERT: D 160 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8487 (mm-30) REVERT: D 184 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8244 (pt0) REVERT: D 199 LYS cc_start: 0.8471 (ptpt) cc_final: 0.8137 (ptmm) REVERT: D 201 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8435 (mp0) REVERT: D 206 ASP cc_start: 0.8487 (t0) cc_final: 0.8076 (t0) REVERT: D 208 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8438 (mtmm) REVERT: D 272 TYR cc_start: 0.8971 (t80) cc_final: 0.8139 (t80) REVERT: D 281 GLN cc_start: 0.8734 (mm110) cc_final: 0.8423 (mm-40) REVERT: D 283 LEU cc_start: 0.8702 (mt) cc_final: 0.8319 (mp) REVERT: D 402 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8274 (mt-10) REVERT: E 75 ASP cc_start: 0.8358 (t0) cc_final: 0.7695 (t0) REVERT: E 77 LEU cc_start: 0.9285 (mt) cc_final: 0.9062 (mm) REVERT: E 113 GLU cc_start: 0.9175 (mp0) cc_final: 0.8905 (mp0) REVERT: E 132 ASP cc_start: 0.7913 (t0) cc_final: 0.7629 (t0) REVERT: E 146 LYS cc_start: 0.8679 (mtpt) cc_final: 0.7996 (mtmp) REVERT: E 160 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8372 (mm-30) REVERT: E 167 ASP cc_start: 0.9416 (p0) cc_final: 0.9059 (p0) REVERT: E 201 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8408 (mp0) REVERT: E 206 ASP cc_start: 0.8439 (t0) cc_final: 0.8153 (t0) REVERT: E 279 LEU cc_start: 0.9078 (tp) cc_final: 0.8864 (tt) REVERT: E 283 LEU cc_start: 0.8694 (mt) cc_final: 0.8296 (mp) outliers start: 52 outliers final: 24 residues processed: 351 average time/residue: 1.1170 time to fit residues: 432.0866 Evaluate side-chains 337 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 309 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 379 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 135 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 221 GLN C 156 ASN C 221 GLN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.078044 restraints weight = 20544.680| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.43 r_work: 0.2796 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13385 Z= 0.191 Angle : 0.533 9.299 18305 Z= 0.259 Chirality : 0.039 0.186 2235 Planarity : 0.004 0.027 2250 Dihedral : 4.734 44.639 2060 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.80 % Allowed : 20.00 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.21), residues: 1600 helix: 2.85 (0.20), residues: 530 sheet: 0.56 (0.24), residues: 475 loop : 0.21 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 112 HIS 0.001 0.000 HIS E 276 PHE 0.020 0.002 PHE A 385 TYR 0.020 0.002 TYR D 176 ARG 0.010 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 331 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8382 (t0) cc_final: 0.8034 (t0) REVERT: A 81 MET cc_start: 0.9017 (ttp) cc_final: 0.8695 (ptt) REVERT: A 132 ASP cc_start: 0.8331 (m-30) cc_final: 0.8117 (t0) REVERT: A 153 THR cc_start: 0.9347 (p) cc_final: 0.9052 (t) REVERT: A 201 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8426 (mp0) REVERT: A 206 ASP cc_start: 0.8475 (t0) cc_final: 0.8143 (t0) REVERT: A 208 LYS cc_start: 0.8606 (ptpt) cc_final: 0.8265 (mtmm) REVERT: A 232 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8343 (ttmm) REVERT: A 272 TYR cc_start: 0.8942 (t80) cc_final: 0.8289 (t80) REVERT: A 281 GLN cc_start: 0.8728 (mm110) cc_final: 0.8327 (pt0) REVERT: A 283 LEU cc_start: 0.8608 (mt) cc_final: 0.8200 (mp) REVERT: A 296 TYR cc_start: 0.8454 (t80) cc_final: 0.8236 (t80) REVERT: A 297 PHE cc_start: 0.8893 (m-80) cc_final: 0.8494 (m-10) REVERT: A 364 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8118 (mt-10) REVERT: B 75 ASP cc_start: 0.8302 (t0) cc_final: 0.7789 (t0) REVERT: B 78 ARG cc_start: 0.8767 (mtp85) cc_final: 0.8562 (mtp85) REVERT: B 129 ASP cc_start: 0.8839 (t0) cc_final: 0.8341 (t0) REVERT: B 146 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8120 (mttp) REVERT: B 201 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8262 (mp0) REVERT: B 206 ASP cc_start: 0.8377 (t0) cc_final: 0.7910 (t0) REVERT: B 232 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8386 (ttmm) REVERT: B 260 GLU cc_start: 0.8927 (pm20) cc_final: 0.8397 (pm20) REVERT: B 281 GLN cc_start: 0.8705 (mm110) cc_final: 0.8316 (pt0) REVERT: B 283 LEU cc_start: 0.8555 (mt) cc_final: 0.8210 (mp) REVERT: C 75 ASP cc_start: 0.8407 (t0) cc_final: 0.7970 (t0) REVERT: C 77 LEU cc_start: 0.9374 (mt) cc_final: 0.9156 (mm) REVERT: C 113 GLU cc_start: 0.9103 (mp0) cc_final: 0.8744 (mp0) REVERT: C 129 ASP cc_start: 0.8833 (t0) cc_final: 0.8231 (t0) REVERT: C 146 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8128 (mtmp) REVERT: C 160 GLU cc_start: 0.8572 (tt0) cc_final: 0.8148 (mm-30) REVERT: C 184 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8329 (pt0) REVERT: C 201 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8475 (mp0) REVERT: C 208 LYS cc_start: 0.8727 (mtmm) cc_final: 0.8428 (mtmm) REVERT: C 238 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8486 (mm) REVERT: C 281 GLN cc_start: 0.8717 (mm110) cc_final: 0.8218 (pt0) REVERT: C 402 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8437 (mt-10) REVERT: D 75 ASP cc_start: 0.8438 (t0) cc_final: 0.7816 (t0) REVERT: D 160 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8546 (mm-30) REVERT: D 184 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8281 (pt0) REVERT: D 199 LYS cc_start: 0.8416 (ptpt) cc_final: 0.8122 (ptmm) REVERT: D 201 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8458 (mp0) REVERT: D 206 ASP cc_start: 0.8473 (t0) cc_final: 0.8113 (t0) REVERT: D 208 LYS cc_start: 0.8727 (mtmm) cc_final: 0.8493 (mtmm) REVERT: D 272 TYR cc_start: 0.8951 (t80) cc_final: 0.8056 (t80) REVERT: D 281 GLN cc_start: 0.8664 (mm110) cc_final: 0.8247 (pt0) REVERT: D 283 LEU cc_start: 0.8736 (mt) cc_final: 0.8237 (mp) REVERT: D 402 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8312 (mt-10) REVERT: E 75 ASP cc_start: 0.8393 (t0) cc_final: 0.7937 (t0) REVERT: E 113 GLU cc_start: 0.9140 (mp0) cc_final: 0.8912 (mp0) REVERT: E 146 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8085 (mttp) REVERT: E 160 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8411 (mm-30) REVERT: E 167 ASP cc_start: 0.9425 (p0) cc_final: 0.9085 (p0) REVERT: E 198 VAL cc_start: 0.9374 (OUTLIER) cc_final: 0.9011 (m) REVERT: E 201 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8371 (mp0) REVERT: E 206 ASP cc_start: 0.8429 (t0) cc_final: 0.8078 (t0) REVERT: E 208 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8235 (mtmm) REVERT: E 227 LYS cc_start: 0.8836 (ptmt) cc_final: 0.8530 (ptpp) REVERT: E 232 LYS cc_start: 0.8797 (ttmt) cc_final: 0.8418 (ttmm) REVERT: E 272 TYR cc_start: 0.8957 (t80) cc_final: 0.8222 (t80) REVERT: E 283 LEU cc_start: 0.8637 (mt) cc_final: 0.8184 (mp) outliers start: 40 outliers final: 20 residues processed: 354 average time/residue: 1.0805 time to fit residues: 422.6135 Evaluate side-chains 353 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 329 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 253 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 32 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 101 optimal weight: 0.0270 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 221 GLN C 156 ASN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.089387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.076043 restraints weight = 20856.863| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.49 r_work: 0.2773 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13385 Z= 0.322 Angle : 0.577 9.445 18305 Z= 0.281 Chirality : 0.041 0.174 2235 Planarity : 0.004 0.035 2250 Dihedral : 4.534 37.029 2060 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.80 % Allowed : 20.49 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.21), residues: 1600 helix: 2.77 (0.20), residues: 525 sheet: 0.73 (0.24), residues: 430 loop : -0.14 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 112 HIS 0.002 0.001 HIS E 103 PHE 0.025 0.002 PHE A 385 TYR 0.025 0.002 TYR B 176 ARG 0.014 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 334 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8584 (tp30) cc_final: 0.8155 (mm-30) REVERT: A 75 ASP cc_start: 0.8367 (t0) cc_final: 0.7962 (t0) REVERT: A 81 MET cc_start: 0.9062 (ttp) cc_final: 0.8773 (ptt) REVERT: A 132 ASP cc_start: 0.8395 (m-30) cc_final: 0.8099 (t0) REVERT: A 146 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8103 (mttp) REVERT: A 201 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8405 (mp0) REVERT: A 206 ASP cc_start: 0.8495 (t0) cc_final: 0.8142 (t0) REVERT: A 208 LYS cc_start: 0.8567 (ptpt) cc_final: 0.8217 (mtmm) REVERT: A 272 TYR cc_start: 0.8939 (t80) cc_final: 0.8278 (t80) REVERT: A 281 GLN cc_start: 0.8792 (mm110) cc_final: 0.8330 (pt0) REVERT: A 283 LEU cc_start: 0.8584 (mt) cc_final: 0.8266 (mp) REVERT: A 296 TYR cc_start: 0.8439 (t80) cc_final: 0.8238 (t80) REVERT: A 297 PHE cc_start: 0.8881 (m-80) cc_final: 0.8574 (m-80) REVERT: A 364 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8094 (mt-10) REVERT: B 75 ASP cc_start: 0.8216 (t0) cc_final: 0.7686 (t0) REVERT: B 129 ASP cc_start: 0.8776 (t0) cc_final: 0.8226 (t0) REVERT: B 201 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8267 (mp0) REVERT: B 206 ASP cc_start: 0.8394 (t0) cc_final: 0.7944 (t0) REVERT: B 260 GLU cc_start: 0.8909 (pm20) cc_final: 0.8361 (pm20) REVERT: B 281 GLN cc_start: 0.8720 (mm110) cc_final: 0.8358 (pt0) REVERT: C 48 GLU cc_start: 0.8493 (tp30) cc_final: 0.8229 (mm-30) REVERT: C 75 ASP cc_start: 0.8342 (t0) cc_final: 0.8036 (t0) REVERT: C 77 LEU cc_start: 0.9403 (mt) cc_final: 0.9176 (mm) REVERT: C 113 GLU cc_start: 0.9130 (mp0) cc_final: 0.8785 (mp0) REVERT: C 124 GLU cc_start: 0.8977 (mp0) cc_final: 0.8646 (mp0) REVERT: C 129 ASP cc_start: 0.8771 (t0) cc_final: 0.8172 (t0) REVERT: C 146 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8014 (mtmp) REVERT: C 160 GLU cc_start: 0.8589 (tt0) cc_final: 0.8062 (tp30) REVERT: C 184 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8283 (pt0) REVERT: C 201 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8446 (mp0) REVERT: C 208 LYS cc_start: 0.8654 (mtmm) cc_final: 0.8400 (mtmm) REVERT: C 232 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8333 (tppp) REVERT: C 281 GLN cc_start: 0.8770 (mm110) cc_final: 0.8282 (pt0) REVERT: C 364 GLU cc_start: 0.8619 (mp0) cc_final: 0.8366 (mt-10) REVERT: C 402 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8408 (mt-10) REVERT: D 48 GLU cc_start: 0.8542 (tp30) cc_final: 0.8253 (mm-30) REVERT: D 75 ASP cc_start: 0.8383 (t0) cc_final: 0.7704 (t0) REVERT: D 160 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8297 (tp30) REVERT: D 184 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8218 (pt0) REVERT: D 199 LYS cc_start: 0.8493 (ptpt) cc_final: 0.8196 (ptmm) REVERT: D 201 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8425 (mp0) REVERT: D 206 ASP cc_start: 0.8481 (t0) cc_final: 0.8074 (t0) REVERT: D 208 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8421 (mtmm) REVERT: D 272 TYR cc_start: 0.8961 (t80) cc_final: 0.8092 (t80) REVERT: D 281 GLN cc_start: 0.8723 (mm110) cc_final: 0.8403 (mm-40) REVERT: D 283 LEU cc_start: 0.8726 (mt) cc_final: 0.8310 (mp) REVERT: D 402 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8313 (mt-10) REVERT: E 75 ASP cc_start: 0.8305 (t0) cc_final: 0.7963 (t0) REVERT: E 113 GLU cc_start: 0.9178 (mp0) cc_final: 0.8930 (mp0) REVERT: E 132 ASP cc_start: 0.7933 (t0) cc_final: 0.7626 (t0) REVERT: E 146 LYS cc_start: 0.8664 (mtpt) cc_final: 0.7990 (mtmp) REVERT: E 160 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8397 (mm-30) REVERT: E 167 ASP cc_start: 0.9426 (p0) cc_final: 0.9084 (p0) REVERT: E 201 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8410 (mp0) REVERT: E 206 ASP cc_start: 0.8434 (t0) cc_final: 0.8062 (t0) REVERT: E 208 LYS cc_start: 0.8757 (mtmm) cc_final: 0.8279 (mtmm) REVERT: E 283 LEU cc_start: 0.8696 (mt) cc_final: 0.8469 (mp) outliers start: 40 outliers final: 21 residues processed: 357 average time/residue: 1.2326 time to fit residues: 482.0141 Evaluate side-chains 344 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 321 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 92 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 221 GLN C 156 ASN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 382 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.089609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.076341 restraints weight = 20486.806| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.43 r_work: 0.2770 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13385 Z= 0.280 Angle : 0.568 9.623 18305 Z= 0.277 Chirality : 0.040 0.142 2235 Planarity : 0.004 0.039 2250 Dihedral : 4.412 31.631 2060 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.52 % Allowed : 20.84 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.21), residues: 1600 helix: 2.72 (0.20), residues: 530 sheet: 0.68 (0.24), residues: 430 loop : -0.06 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 112 HIS 0.002 0.000 HIS E 276 PHE 0.022 0.002 PHE A 385 TYR 0.020 0.002 TYR D 176 ARG 0.017 0.001 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 331 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8382 (t0) cc_final: 0.7997 (t0) REVERT: A 81 MET cc_start: 0.9041 (ttp) cc_final: 0.8754 (ptt) REVERT: A 146 LYS cc_start: 0.8755 (mtpt) cc_final: 0.8191 (mttp) REVERT: A 201 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8440 (mp0) REVERT: A 206 ASP cc_start: 0.8512 (t0) cc_final: 0.8192 (t0) REVERT: A 232 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8282 (ttmm) REVERT: A 272 TYR cc_start: 0.8973 (t80) cc_final: 0.8335 (t80) REVERT: A 281 GLN cc_start: 0.8795 (mm110) cc_final: 0.8395 (pt0) REVERT: A 283 LEU cc_start: 0.8590 (mt) cc_final: 0.8200 (mp) REVERT: A 297 PHE cc_start: 0.8930 (m-80) cc_final: 0.8571 (m-10) REVERT: A 364 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8118 (mt-10) REVERT: B 48 GLU cc_start: 0.8652 (tp30) cc_final: 0.8421 (tp30) REVERT: B 75 ASP cc_start: 0.8308 (t0) cc_final: 0.7795 (t0) REVERT: B 129 ASP cc_start: 0.8807 (t0) cc_final: 0.8402 (t0) REVERT: B 146 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8132 (mttp) REVERT: B 201 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8312 (mp0) REVERT: B 206 ASP cc_start: 0.8396 (t0) cc_final: 0.7979 (t0) REVERT: B 232 LYS cc_start: 0.8708 (ttmt) cc_final: 0.8383 (ttmm) REVERT: B 260 GLU cc_start: 0.8927 (pm20) cc_final: 0.8385 (pm20) REVERT: B 281 GLN cc_start: 0.8717 (mm110) cc_final: 0.8358 (pt0) REVERT: B 364 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8473 (mt-10) REVERT: C 48 GLU cc_start: 0.8544 (tp30) cc_final: 0.8284 (mm-30) REVERT: C 75 ASP cc_start: 0.8414 (t0) cc_final: 0.7950 (t0) REVERT: C 77 LEU cc_start: 0.9434 (mt) cc_final: 0.9221 (mm) REVERT: C 81 MET cc_start: 0.9126 (ttp) cc_final: 0.8856 (ptm) REVERT: C 113 GLU cc_start: 0.9123 (mp0) cc_final: 0.8815 (mp0) REVERT: C 124 GLU cc_start: 0.8994 (mp0) cc_final: 0.8686 (mp0) REVERT: C 129 ASP cc_start: 0.8827 (t0) cc_final: 0.8278 (t0) REVERT: C 146 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8140 (mtmp) REVERT: C 160 GLU cc_start: 0.8572 (tt0) cc_final: 0.8091 (tp30) REVERT: C 201 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8466 (mp0) REVERT: C 232 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8365 (tppp) REVERT: C 281 GLN cc_start: 0.8738 (mm110) cc_final: 0.8266 (pt0) REVERT: C 364 GLU cc_start: 0.8668 (mp0) cc_final: 0.8435 (mt-10) REVERT: C 402 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8443 (mt-10) REVERT: D 75 ASP cc_start: 0.8443 (t0) cc_final: 0.7789 (t0) REVERT: D 146 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8130 (mttp) REVERT: D 160 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8600 (mm-30) REVERT: D 184 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8266 (pt0) REVERT: D 199 LYS cc_start: 0.8509 (ptpt) cc_final: 0.8221 (ptmm) REVERT: D 201 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8454 (mp0) REVERT: D 206 ASP cc_start: 0.8492 (t0) cc_final: 0.8115 (t0) REVERT: D 208 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8465 (mtmm) REVERT: D 232 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8330 (tppp) REVERT: D 281 GLN cc_start: 0.8772 (mm110) cc_final: 0.8473 (mm-40) REVERT: D 283 LEU cc_start: 0.8693 (mt) cc_final: 0.8159 (mp) REVERT: D 402 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8368 (mt-10) REVERT: E 75 ASP cc_start: 0.8397 (t0) cc_final: 0.7942 (t0) REVERT: E 113 GLU cc_start: 0.9164 (mp0) cc_final: 0.8630 (mp0) REVERT: E 132 ASP cc_start: 0.7922 (t0) cc_final: 0.7633 (t0) REVERT: E 146 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8093 (mtmp) REVERT: E 160 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8443 (mm-30) REVERT: E 167 ASP cc_start: 0.9449 (p0) cc_final: 0.9097 (p0) REVERT: E 201 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8422 (mp0) REVERT: E 206 ASP cc_start: 0.8454 (t0) cc_final: 0.8106 (t0) REVERT: E 208 LYS cc_start: 0.8838 (mtmm) cc_final: 0.8395 (mtmm) REVERT: E 232 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8414 (ttmm) REVERT: E 283 LEU cc_start: 0.8701 (mt) cc_final: 0.8360 (mp) outliers start: 36 outliers final: 23 residues processed: 355 average time/residue: 1.1649 time to fit residues: 454.1455 Evaluate side-chains 334 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 309 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 372 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 49 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 136 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 221 GLN C 156 ASN C 221 GLN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.091845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.078609 restraints weight = 20436.293| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.43 r_work: 0.2810 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13385 Z= 0.176 Angle : 0.562 9.682 18305 Z= 0.271 Chirality : 0.039 0.142 2235 Planarity : 0.004 0.026 2250 Dihedral : 4.182 25.415 2060 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.89 % Allowed : 21.61 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.21), residues: 1600 helix: 2.96 (0.20), residues: 525 sheet: 0.72 (0.25), residues: 430 loop : -0.02 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 362 HIS 0.001 0.000 HIS A 276 PHE 0.020 0.002 PHE A 385 TYR 0.032 0.002 TYR D 176 ARG 0.011 0.000 ARG C 257 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 327 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8647 (tp30) cc_final: 0.8220 (mm-30) REVERT: A 75 ASP cc_start: 0.8381 (t0) cc_final: 0.8008 (t0) REVERT: A 81 MET cc_start: 0.8973 (ttp) cc_final: 0.8668 (ptt) REVERT: A 146 LYS cc_start: 0.8738 (mtpt) cc_final: 0.8177 (mttp) REVERT: A 153 THR cc_start: 0.9341 (p) cc_final: 0.9038 (t) REVERT: A 184 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8425 (mt-10) REVERT: A 201 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8408 (mp0) REVERT: A 206 ASP cc_start: 0.8433 (t0) cc_final: 0.8128 (t0) REVERT: A 208 LYS cc_start: 0.8730 (ptpp) cc_final: 0.8209 (mtmm) REVERT: A 232 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8274 (ttmm) REVERT: A 272 TYR cc_start: 0.8909 (t80) cc_final: 0.8271 (t80) REVERT: A 283 LEU cc_start: 0.8641 (mt) cc_final: 0.8278 (mp) REVERT: A 297 PHE cc_start: 0.8876 (m-80) cc_final: 0.8506 (m-10) REVERT: A 364 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8218 (mp0) REVERT: B 75 ASP cc_start: 0.8257 (t0) cc_final: 0.7793 (t0) REVERT: B 129 ASP cc_start: 0.8823 (t0) cc_final: 0.8415 (t0) REVERT: B 146 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8138 (mttp) REVERT: B 160 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8458 (mm-30) REVERT: B 201 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8274 (mp0) REVERT: B 206 ASP cc_start: 0.8364 (t0) cc_final: 0.7916 (t0) REVERT: B 232 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8388 (ttmm) REVERT: B 260 GLU cc_start: 0.8876 (pm20) cc_final: 0.8360 (pm20) REVERT: C 75 ASP cc_start: 0.8407 (t0) cc_final: 0.7937 (t0) REVERT: C 77 LEU cc_start: 0.9405 (mt) cc_final: 0.9204 (mm) REVERT: C 81 MET cc_start: 0.9106 (ttp) cc_final: 0.8854 (ptm) REVERT: C 129 ASP cc_start: 0.8834 (t0) cc_final: 0.8208 (t0) REVERT: C 146 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8128 (mtmp) REVERT: C 160 GLU cc_start: 0.8574 (tt0) cc_final: 0.8147 (mm-30) REVERT: C 184 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8342 (pt0) REVERT: C 201 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8398 (mp0) REVERT: C 232 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8412 (tppp) REVERT: C 260 GLU cc_start: 0.8882 (pm20) cc_final: 0.8400 (pm20) REVERT: C 402 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8458 (mt-10) REVERT: D 75 ASP cc_start: 0.8460 (t0) cc_final: 0.7826 (t0) REVERT: D 146 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8104 (mttp) REVERT: D 184 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8280 (pt0) REVERT: D 199 LYS cc_start: 0.8448 (ptpt) cc_final: 0.8127 (ptmm) REVERT: D 201 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8446 (mp0) REVERT: D 206 ASP cc_start: 0.8462 (t0) cc_final: 0.8118 (t0) REVERT: D 208 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8446 (mtmm) REVERT: D 232 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8310 (tppp) REVERT: D 272 TYR cc_start: 0.8952 (t80) cc_final: 0.8101 (t80) REVERT: D 281 GLN cc_start: 0.8711 (mm110) cc_final: 0.8337 (pt0) REVERT: D 283 LEU cc_start: 0.8682 (mt) cc_final: 0.8159 (mp) REVERT: D 402 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8338 (mt-10) REVERT: E 75 ASP cc_start: 0.8381 (t0) cc_final: 0.7986 (t0) REVERT: E 113 GLU cc_start: 0.9126 (mp0) cc_final: 0.8751 (mp0) REVERT: E 132 ASP cc_start: 0.7815 (t0) cc_final: 0.7556 (t0) REVERT: E 146 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8080 (mttp) REVERT: E 160 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8435 (mm-30) REVERT: E 167 ASP cc_start: 0.9440 (p0) cc_final: 0.9112 (p0) REVERT: E 201 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8405 (mp0) REVERT: E 206 ASP cc_start: 0.8423 (t0) cc_final: 0.8100 (t0) REVERT: E 208 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8394 (mtmm) REVERT: E 227 LYS cc_start: 0.8841 (ptmt) cc_final: 0.8533 (ptpp) REVERT: E 232 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8400 (ttmm) REVERT: E 283 LEU cc_start: 0.8664 (mt) cc_final: 0.8349 (mp) outliers start: 27 outliers final: 19 residues processed: 345 average time/residue: 1.1109 time to fit residues: 422.9326 Evaluate side-chains 336 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 316 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 305 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 154 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 221 GLN C 156 ASN C 382 GLN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 382 GLN E 156 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.089105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.075772 restraints weight = 20573.992| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.43 r_work: 0.2757 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13385 Z= 0.381 Angle : 0.608 9.724 18305 Z= 0.300 Chirality : 0.042 0.248 2235 Planarity : 0.004 0.027 2250 Dihedral : 4.278 23.308 2060 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.24 % Allowed : 21.12 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.21), residues: 1600 helix: 2.68 (0.20), residues: 525 sheet: 0.61 (0.24), residues: 430 loop : -0.11 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 112 HIS 0.002 0.001 HIS E 103 PHE 0.023 0.002 PHE A 385 TYR 0.059 0.003 TYR D 176 ARG 0.015 0.001 ARG C 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9567.40 seconds wall clock time: 170 minutes 21.58 seconds (10221.58 seconds total)