Starting phenix.real_space_refine on Thu May 15 11:36:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yx8_39650/05_2025/8yx8_39650.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yx8_39650/05_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_39650/05_2025/8yx8_39650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yx8_39650/05_2025/8yx8_39650.map" model { file = "/net/cci-nas-00/data/ceres_data/8yx8_39650/05_2025/8yx8_39650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yx8_39650/05_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-5687/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: 7.66, per 1000 atoms: 0.59 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: 3.19 Conformation dependent library (CDL) restraints added in 1.6 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: 1.38 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: 3.90 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: 1.660 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.400 Find NCS groups from input model: 0.260 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:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.630 ------------------------------------------------------------------------------- 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 13410 Z= 0.338 Angle : 0.580 5.495 18370 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 10) link_NAG-ASN : angle 1.11217 ( 30) link_BETA1-4 : bond 0.00300 ( 5) link_BETA1-4 : angle 0.98132 ( 15) hydrogen bonds : bond 0.12231 ( 680) hydrogen bonds : angle 4.99996 ( 2100) SS BOND : bond 0.00031 ( 10) SS BOND : angle 0.51145 ( 20) covalent geometry : bond 0.00674 (13385) covalent geometry : angle 0.57846 (18305) *********************** 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 : 1.489 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: 1.0069 time to fit residues: 545.9005 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 : 1.491 ------------------------------------------------------------------------------- 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 13410 Z= 0.123 Angle : 0.519 7.656 18370 Z= 0.254 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 10) link_NAG-ASN : angle 1.42851 ( 30) link_BETA1-4 : bond 0.00221 ( 5) link_BETA1-4 : angle 1.67263 ( 15) hydrogen bonds : bond 0.04331 ( 680) hydrogen bonds : angle 4.15374 ( 2100) SS BOND : bond 0.00341 ( 10) SS BOND : angle 1.02867 ( 20) covalent geometry : bond 0.00269 (13385) covalent geometry : angle 0.51358 (18305) *********************** 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 : 1.322 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: 1.1243 time to fit residues: 477.4031 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 : 1.439 ------------------------------------------------------------------------------- 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 13410 Z= 0.217 Angle : 0.560 8.406 18370 Z= 0.274 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 10) link_NAG-ASN : angle 1.40002 ( 30) link_BETA1-4 : bond 0.00274 ( 5) link_BETA1-4 : angle 1.40366 ( 15) hydrogen bonds : bond 0.04293 ( 680) hydrogen bonds : angle 4.22282 ( 2100) SS BOND : bond 0.00301 ( 10) SS BOND : angle 1.20843 ( 20) covalent geometry : bond 0.00488 (13385) covalent geometry : angle 0.55511 (18305) *********************** 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 : 1.460 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: 1.0483 time to fit residues: 427.9513 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 : 1.398 ------------------------------------------------------------------------------- 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: 0.4980 chunk 83 optimal weight: 0.9990 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: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3218 r_free = 0.3218 target = 0.096111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.081490 restraints weight = 20012.466| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.90 r_work: 0.2859 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 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 = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13410 Z= 0.120 Angle : 0.515 8.475 18370 Z= 0.251 Chirality : 0.039 0.181 2235 Planarity : 0.004 0.029 2250 Dihedral : 5.419 55.605 2062 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 1.95 (0.21), residues: 1600 helix: 2.93 (0.20), residues: 530 sheet: 0.83 (0.24), residues: 475 loop : 0.24 (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 0.009 0.000 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 10) link_NAG-ASN : angle 1.16323 ( 30) link_BETA1-4 : bond 0.00233 ( 5) link_BETA1-4 : angle 1.27251 ( 15) hydrogen bonds : bond 0.03954 ( 680) hydrogen bonds : angle 4.09514 ( 2100) SS BOND : bond 0.00285 ( 10) SS BOND : angle 0.91906 ( 20) covalent geometry : bond 0.00261 (13385) covalent geometry : angle 0.51171 (18305) *********************** 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 376 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 331 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8096 (t0) cc_final: 0.7656 (t0) REVERT: A 78 ARG cc_start: 0.8578 (mtp85) cc_final: 0.8340 (mtp85) REVERT: A 141 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: A 153 THR cc_start: 0.9125 (p) cc_final: 0.8866 (t) REVERT: A 201 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8178 (mp0) REVERT: A 206 ASP cc_start: 0.8291 (t0) cc_final: 0.7851 (t0) REVERT: A 208 LYS cc_start: 0.8311 (ptpt) cc_final: 0.8038 (mtmm) REVERT: A 232 LYS cc_start: 0.8490 (ttmt) cc_final: 0.8067 (ttmm) REVERT: A 272 TYR cc_start: 0.8692 (t80) cc_final: 0.8033 (t80) REVERT: A 281 GLN cc_start: 0.8680 (mm110) cc_final: 0.8261 (pt0) REVERT: A 283 LEU cc_start: 0.8563 (mt) cc_final: 0.8242 (mp) REVERT: A 297 PHE cc_start: 0.8553 (m-80) cc_final: 0.8137 (m-10) REVERT: A 364 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7687 (mt-10) REVERT: B 75 ASP cc_start: 0.7828 (t0) cc_final: 0.7272 (t0) REVERT: B 129 ASP cc_start: 0.8542 (t0) cc_final: 0.8026 (t0) REVERT: B 146 LYS cc_start: 0.8403 (mtmt) cc_final: 0.7588 (mttp) REVERT: B 160 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8045 (mm-30) REVERT: B 199 LYS cc_start: 0.8012 (ptpt) cc_final: 0.7756 (ptmt) REVERT: B 201 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8059 (mp0) REVERT: B 206 ASP cc_start: 0.8248 (t0) cc_final: 0.7649 (t0) REVERT: B 279 LEU cc_start: 0.8928 (tp) cc_final: 0.8690 (tt) REVERT: B 281 GLN cc_start: 0.8724 (mm110) cc_final: 0.8335 (pt0) REVERT: B 283 LEU cc_start: 0.8527 (mt) cc_final: 0.8152 (mp) REVERT: B 296 TYR cc_start: 0.8332 (t80) cc_final: 0.8091 (t80) REVERT: C 75 ASP cc_start: 0.7977 (t0) cc_final: 0.7309 (t0) REVERT: C 113 GLU cc_start: 0.9053 (mp0) cc_final: 0.8595 (mp0) REVERT: C 129 ASP cc_start: 0.8586 (t0) cc_final: 0.8107 (t0) REVERT: C 146 LYS cc_start: 0.8377 (mtpt) cc_final: 0.7691 (mtmp) REVERT: C 160 GLU cc_start: 0.8513 (tt0) cc_final: 0.7919 (mm-30) REVERT: C 184 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7718 (pt0) REVERT: C 201 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8264 (mp0) REVERT: C 208 LYS cc_start: 0.8359 (ptpt) cc_final: 0.8094 (mtmm) REVERT: C 232 LYS cc_start: 0.8550 (ttmt) cc_final: 0.8316 (ttmt) REVERT: C 233 SER cc_start: 0.8685 (m) cc_final: 0.8392 (p) REVERT: C 281 GLN cc_start: 0.8714 (mm110) cc_final: 0.8163 (pt0) REVERT: C 283 LEU cc_start: 0.8681 (mt) cc_final: 0.8360 (mp) REVERT: C 402 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8240 (mt-10) REVERT: D 75 ASP cc_start: 0.8095 (t0) cc_final: 0.7391 (t0) REVERT: D 77 LEU cc_start: 0.9173 (mt) cc_final: 0.8931 (mm) REVERT: D 78 ARG cc_start: 0.8764 (mtp85) cc_final: 0.8453 (mtp85) REVERT: D 160 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8323 (mm-30) REVERT: D 184 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7726 (pt0) REVERT: D 201 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8181 (mp0) REVERT: D 206 ASP cc_start: 0.8234 (t0) cc_final: 0.7819 (t0) REVERT: D 208 LYS cc_start: 0.8463 (mtmm) cc_final: 0.8130 (mtmm) REVERT: D 281 GLN cc_start: 0.8647 (mm110) cc_final: 0.8110 (pt0) REVERT: D 283 LEU cc_start: 0.8635 (mt) cc_final: 0.8273 (mp) REVERT: D 402 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8146 (mt-10) REVERT: E 75 ASP cc_start: 0.8037 (t0) cc_final: 0.7391 (t0) REVERT: E 77 LEU cc_start: 0.9089 (mt) cc_final: 0.8837 (mm) REVERT: E 78 ARG cc_start: 0.8649 (mtp85) cc_final: 0.8429 (mtp85) REVERT: E 113 GLU cc_start: 0.9014 (mp0) cc_final: 0.8552 (mp0) REVERT: E 146 LYS cc_start: 0.8390 (mtpt) cc_final: 0.7653 (mtmp) REVERT: E 160 GLU cc_start: 0.8622 (tt0) cc_final: 0.8129 (mm-30) REVERT: E 184 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7904 (mt-10) REVERT: E 198 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.8953 (m) REVERT: E 201 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8162 (mp0) REVERT: E 206 ASP cc_start: 0.8211 (t0) cc_final: 0.7771 (t0) REVERT: E 208 LYS cc_start: 0.8290 (ptpt) cc_final: 0.7851 (mtmm) REVERT: E 279 LEU cc_start: 0.8930 (tp) cc_final: 0.8720 (tt) REVERT: E 283 LEU cc_start: 0.8519 (mt) cc_final: 0.8070 (mp) outliers start: 45 outliers final: 22 residues processed: 354 average time/residue: 0.9909 time to fit residues: 388.7504 Evaluate side-chains 344 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 319 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 D residue 253 LEU Chi-restraints excluded: chain D residue 305 PHE 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: 1.9990 chunk 151 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 111 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3156 r_free = 0.3156 target = 0.091392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.078127 restraints weight = 20677.633| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.50 r_work: 0.2814 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13410 Z= 0.170 Angle : 0.529 8.857 18370 Z= 0.257 Chirality : 0.040 0.140 2235 Planarity : 0.004 0.034 2250 Dihedral : 5.132 52.557 2060 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.29 % Allowed : 17.62 % Favored : 79.09 % 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: 1.84 (0.21), residues: 1600 helix: 2.87 (0.20), residues: 530 sheet: 0.70 (0.24), residues: 475 loop : 0.21 (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 E 103 PHE 0.019 0.002 PHE E 72 TYR 0.017 0.002 TYR D 176 ARG 0.010 0.000 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 10) link_NAG-ASN : angle 1.24691 ( 30) link_BETA1-4 : bond 0.00147 ( 5) link_BETA1-4 : angle 1.29640 ( 15) hydrogen bonds : bond 0.04003 ( 680) hydrogen bonds : angle 4.12966 ( 2100) SS BOND : bond 0.00381 ( 10) SS BOND : angle 1.25507 ( 20) covalent geometry : bond 0.00380 (13385) covalent geometry : angle 0.52458 (18305) *********************** 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 378 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 331 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.8400 (t0) cc_final: 0.8015 (t0) REVERT: A 160 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8333 (mm-30) REVERT: A 201 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8414 (mp0) REVERT: A 206 ASP cc_start: 0.8469 (t0) cc_final: 0.8075 (t0) REVERT: A 207 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9117 (mp) REVERT: A 208 LYS cc_start: 0.8567 (ptpt) cc_final: 0.8283 (mtmm) REVERT: A 232 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8315 (ttmm) REVERT: A 272 TYR cc_start: 0.8926 (t80) cc_final: 0.8368 (t80) REVERT: A 281 GLN cc_start: 0.8719 (mm110) cc_final: 0.8315 (pt0) REVERT: A 283 LEU cc_start: 0.8577 (mt) cc_final: 0.8237 (mp) REVERT: A 297 PHE cc_start: 0.8858 (m-80) cc_final: 0.8525 (m-10) REVERT: A 364 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8005 (mt-10) REVERT: B 75 ASP cc_start: 0.8244 (t0) cc_final: 0.7734 (t0) REVERT: B 129 ASP cc_start: 0.8793 (t0) cc_final: 0.8291 (t0) REVERT: B 146 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8013 (mttp) REVERT: B 160 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8347 (mm-30) REVERT: B 201 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8281 (mp0) REVERT: B 206 ASP cc_start: 0.8392 (t0) cc_final: 0.7856 (t0) REVERT: B 279 LEU cc_start: 0.9043 (tp) cc_final: 0.8780 (tt) REVERT: B 281 GLN cc_start: 0.8773 (mm110) cc_final: 0.8374 (pt0) REVERT: B 283 LEU cc_start: 0.8548 (mt) cc_final: 0.8199 (mp) REVERT: B 296 TYR cc_start: 0.8574 (t80) cc_final: 0.8361 (t80) REVERT: C 75 ASP cc_start: 0.8336 (t0) cc_final: 0.7720 (t0) REVERT: C 77 LEU cc_start: 0.9380 (mt) cc_final: 0.9165 (mm) REVERT: C 113 GLU cc_start: 0.9089 (mp0) cc_final: 0.8702 (mp0) REVERT: C 129 ASP cc_start: 0.8794 (t0) cc_final: 0.8306 (t0) REVERT: C 146 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8040 (mtmp) REVERT: C 160 GLU cc_start: 0.8577 (tt0) cc_final: 0.8123 (mm-30) REVERT: C 184 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8148 (pt0) REVERT: C 201 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8475 (mp0) REVERT: C 233 SER cc_start: 0.8802 (m) cc_final: 0.8581 (p) REVERT: C 281 GLN cc_start: 0.8750 (mm110) cc_final: 0.8239 (pt0) REVERT: C 283 LEU cc_start: 0.8664 (mt) cc_final: 0.8344 (mp) REVERT: C 402 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8383 (mt-10) REVERT: D 75 ASP cc_start: 0.8393 (t0) cc_final: 0.7743 (t0) REVERT: D 77 LEU cc_start: 0.9333 (mt) cc_final: 0.9129 (mm) REVERT: D 78 ARG cc_start: 0.8976 (mtp85) cc_final: 0.8682 (mtp85) REVERT: D 160 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8537 (mm-30) REVERT: D 184 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8375 (mt-10) REVERT: D 199 LYS cc_start: 0.8403 (ptpt) cc_final: 0.8119 (ptmm) REVERT: D 201 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8421 (mp0) REVERT: D 206 ASP cc_start: 0.8447 (t0) cc_final: 0.8098 (t0) REVERT: D 208 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8484 (mtmm) REVERT: D 272 TYR cc_start: 0.8926 (t80) cc_final: 0.8000 (t80) REVERT: D 281 GLN cc_start: 0.8666 (mm110) cc_final: 0.8169 (pt0) REVERT: D 283 LEU cc_start: 0.8711 (mt) cc_final: 0.8401 (mp) REVERT: D 402 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8312 (mt-10) REVERT: E 75 ASP cc_start: 0.8369 (t0) cc_final: 0.7748 (t0) REVERT: E 77 LEU cc_start: 0.9283 (mt) cc_final: 0.9063 (mm) REVERT: E 78 ARG cc_start: 0.8858 (mtp85) cc_final: 0.8647 (mtp85) REVERT: E 113 GLU cc_start: 0.9120 (mp0) cc_final: 0.8675 (mp0) REVERT: E 146 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8004 (mtmp) REVERT: E 160 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8307 (mm-30) REVERT: E 188 GLN cc_start: 0.8257 (mt0) cc_final: 0.8004 (tt0) REVERT: E 198 VAL cc_start: 0.9355 (OUTLIER) cc_final: 0.9033 (m) REVERT: E 201 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8385 (mp0) REVERT: E 206 ASP cc_start: 0.8422 (t0) cc_final: 0.8067 (t0) REVERT: E 208 LYS cc_start: 0.8556 (ptpt) cc_final: 0.8129 (mtmm) REVERT: E 279 LEU cc_start: 0.9065 (tp) cc_final: 0.8860 (tt) REVERT: E 283 LEU cc_start: 0.8642 (mt) cc_final: 0.8210 (mp) outliers start: 47 outliers final: 26 residues processed: 360 average time/residue: 1.0006 time to fit residues: 398.8405 Evaluate side-chains 368 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 338 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 235 ILE Chi-restraints excluded: chain C residue 237 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 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 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: 3.9990 chunk 125 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 221 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.091649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.078700 restraints weight = 20710.586| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.41 r_work: 0.2808 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13410 Z= 0.136 Angle : 0.523 8.995 18370 Z= 0.254 Chirality : 0.039 0.140 2235 Planarity : 0.004 0.027 2250 Dihedral : 4.941 50.138 2060 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.43 % Allowed : 18.11 % Favored : 78.46 % 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: 1.86 (0.21), residues: 1600 helix: 2.92 (0.20), residues: 530 sheet: 0.66 (0.24), residues: 475 loop : 0.23 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 112 HIS 0.001 0.000 HIS E 276 PHE 0.017 0.002 PHE E 385 TYR 0.024 0.002 TYR D 176 ARG 0.008 0.000 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00021 ( 10) link_NAG-ASN : angle 1.19947 ( 30) link_BETA1-4 : bond 0.00244 ( 5) link_BETA1-4 : angle 1.26422 ( 15) hydrogen bonds : bond 0.03908 ( 680) hydrogen bonds : angle 4.08809 ( 2100) SS BOND : bond 0.00348 ( 10) SS BOND : angle 1.05341 ( 20) covalent geometry : bond 0.00299 (13385) covalent geometry : angle 0.51897 (18305) *********************** 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 397 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 348 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8616 (tp30) cc_final: 0.8194 (mm-30) REVERT: A 75 ASP cc_start: 0.8439 (t0) cc_final: 0.8088 (t0) REVERT: A 153 THR cc_start: 0.9328 (p) cc_final: 0.9059 (t) REVERT: A 201 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8462 (mp0) REVERT: A 206 ASP cc_start: 0.8445 (t0) cc_final: 0.8090 (t0) REVERT: A 208 LYS cc_start: 0.8612 (ptpt) cc_final: 0.8300 (mtmm) REVERT: A 272 TYR cc_start: 0.8945 (t80) cc_final: 0.8348 (t80) REVERT: A 281 GLN cc_start: 0.8706 (mm110) cc_final: 0.8336 (pt0) REVERT: A 283 LEU cc_start: 0.8579 (mt) cc_final: 0.8167 (mp) REVERT: A 297 PHE cc_start: 0.8893 (m-80) cc_final: 0.8501 (m-10) REVERT: A 364 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8099 (mp0) REVERT: B 48 GLU cc_start: 0.8637 (tp30) cc_final: 0.8267 (mm-30) REVERT: B 75 ASP cc_start: 0.8297 (t0) cc_final: 0.7796 (t0) REVERT: B 129 ASP cc_start: 0.8849 (t0) cc_final: 0.8336 (t0) REVERT: B 146 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8095 (mttp) REVERT: B 201 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8297 (mp0) REVERT: B 206 ASP cc_start: 0.8394 (t0) cc_final: 0.7887 (t0) REVERT: B 232 LYS cc_start: 0.8727 (ttmt) cc_final: 0.8407 (ttmm) REVERT: B 279 LEU cc_start: 0.9048 (tp) cc_final: 0.8808 (tt) REVERT: B 281 GLN cc_start: 0.8747 (mm110) cc_final: 0.8356 (pt0) REVERT: B 283 LEU cc_start: 0.8497 (mt) cc_final: 0.8138 (mp) REVERT: B 310 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8697 (pp20) REVERT: C 75 ASP cc_start: 0.8391 (t0) cc_final: 0.7795 (t0) REVERT: C 113 GLU cc_start: 0.9084 (mp0) cc_final: 0.8726 (mp0) REVERT: C 129 ASP cc_start: 0.8834 (t0) cc_final: 0.8312 (t0) REVERT: C 146 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8108 (mtmp) REVERT: C 160 GLU cc_start: 0.8562 (tt0) cc_final: 0.8151 (mm-30) REVERT: C 184 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8167 (pt0) REVERT: C 201 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8449 (mp0) REVERT: C 208 LYS cc_start: 0.8684 (mtmm) cc_final: 0.8378 (mtmm) REVERT: C 281 GLN cc_start: 0.8705 (mm110) cc_final: 0.8224 (pt0) REVERT: C 283 LEU cc_start: 0.8632 (mt) cc_final: 0.8343 (mp) REVERT: C 402 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8416 (mt-10) REVERT: D 75 ASP cc_start: 0.8448 (t0) cc_final: 0.7792 (t0) REVERT: D 78 ARG cc_start: 0.8986 (mtp85) cc_final: 0.8703 (mtp85) REVERT: D 160 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8565 (mm-30) REVERT: D 184 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8210 (pt0) REVERT: D 199 LYS cc_start: 0.8386 (ptpt) cc_final: 0.8108 (ptmm) REVERT: D 201 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8456 (mp0) REVERT: D 206 ASP cc_start: 0.8460 (t0) cc_final: 0.8107 (t0) REVERT: D 208 LYS cc_start: 0.8731 (mtmm) cc_final: 0.8505 (mtmm) REVERT: D 272 TYR cc_start: 0.8930 (t80) cc_final: 0.8038 (t80) REVERT: D 281 GLN cc_start: 0.8650 (mm110) cc_final: 0.8186 (pt0) REVERT: D 283 LEU cc_start: 0.8712 (mt) cc_final: 0.8258 (mp) REVERT: D 402 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8349 (mt-10) REVERT: E 75 ASP cc_start: 0.8398 (t0) cc_final: 0.7783 (t0) REVERT: E 113 GLU cc_start: 0.9120 (mp0) cc_final: 0.8716 (mp0) REVERT: E 146 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8080 (mtmp) REVERT: E 160 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8362 (mm-30) REVERT: E 201 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8395 (mp0) REVERT: E 206 ASP cc_start: 0.8401 (t0) cc_final: 0.8062 (t0) REVERT: E 208 LYS cc_start: 0.8604 (ptpt) cc_final: 0.8174 (mtmm) REVERT: E 232 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8424 (ttmm) REVERT: E 272 TYR cc_start: 0.8952 (t80) cc_final: 0.8255 (t80) REVERT: E 279 LEU cc_start: 0.9113 (tp) cc_final: 0.8906 (tt) REVERT: E 283 LEU cc_start: 0.8621 (mt) cc_final: 0.8286 (mp) outliers start: 49 outliers final: 28 residues processed: 376 average time/residue: 1.0701 time to fit residues: 443.7835 Evaluate side-chains 354 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 324 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 142 ASP 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 117 THR 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 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 372 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 136 optimal weight: 0.0020 chunk 157 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 B 221 GLN B 382 GLN C 156 ASN C 221 GLN D 221 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.079266 restraints weight = 20499.380| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.51 r_work: 0.2822 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 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 = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13410 Z= 0.119 Angle : 0.525 9.316 18370 Z= 0.252 Chirality : 0.039 0.153 2235 Planarity : 0.004 0.034 2250 Dihedral : 4.616 44.815 2060 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.08 % Allowed : 19.37 % Favored : 77.55 % 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: 1.84 (0.21), residues: 1600 helix: 2.97 (0.20), residues: 530 sheet: 0.79 (0.24), residues: 450 loop : 0.04 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 112 HIS 0.002 0.000 HIS E 276 PHE 0.021 0.002 PHE C 297 TYR 0.022 0.002 TYR D 176 ARG 0.009 0.000 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 10) link_NAG-ASN : angle 1.15103 ( 30) link_BETA1-4 : bond 0.00263 ( 5) link_BETA1-4 : angle 1.26307 ( 15) hydrogen bonds : bond 0.03838 ( 680) hydrogen bonds : angle 4.04607 ( 2100) SS BOND : bond 0.00459 ( 10) SS BOND : angle 0.95577 ( 20) covalent geometry : bond 0.00260 (13385) covalent geometry : angle 0.52133 (18305) *********************** 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 383 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 339 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8588 (tp30) cc_final: 0.8147 (mm-30) REVERT: A 75 ASP cc_start: 0.8316 (t0) cc_final: 0.7949 (t0) REVERT: A 81 MET cc_start: 0.9013 (ttp) cc_final: 0.8667 (ptt) REVERT: A 153 THR cc_start: 0.9300 (p) cc_final: 0.9019 (t) REVERT: A 184 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8333 (mt-10) REVERT: A 201 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8367 (mp0) REVERT: A 206 ASP cc_start: 0.8440 (t0) cc_final: 0.8075 (t0) REVERT: A 208 LYS cc_start: 0.8528 (ptpt) cc_final: 0.8254 (mtmm) REVERT: A 232 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8239 (ttmm) REVERT: A 272 TYR cc_start: 0.8870 (t80) cc_final: 0.8294 (t80) REVERT: A 283 LEU cc_start: 0.8559 (mt) cc_final: 0.8121 (mp) REVERT: A 296 TYR cc_start: 0.8385 (t80) cc_final: 0.8179 (t80) REVERT: A 297 PHE cc_start: 0.8789 (m-80) cc_final: 0.8428 (m-10) REVERT: A 364 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8130 (mp0) REVERT: B 75 ASP cc_start: 0.8199 (t0) cc_final: 0.7700 (t0) REVERT: B 129 ASP cc_start: 0.8769 (t0) cc_final: 0.8218 (t0) REVERT: B 146 LYS cc_start: 0.8720 (mtmt) cc_final: 0.7989 (mttp) REVERT: B 199 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7902 (ptmm) REVERT: B 201 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8212 (mp0) REVERT: B 206 ASP cc_start: 0.8363 (t0) cc_final: 0.7848 (t0) REVERT: B 232 LYS cc_start: 0.8626 (ttmt) cc_final: 0.8309 (ttmm) REVERT: B 260 GLU cc_start: 0.8843 (pm20) cc_final: 0.8327 (pm20) REVERT: B 281 GLN cc_start: 0.8667 (mm110) cc_final: 0.8293 (pt0) REVERT: B 283 LEU cc_start: 0.8573 (mt) cc_final: 0.8193 (mp) REVERT: C 75 ASP cc_start: 0.8306 (t0) cc_final: 0.7686 (t0) REVERT: C 113 GLU cc_start: 0.9108 (mp0) cc_final: 0.8738 (mp0) REVERT: C 129 ASP cc_start: 0.8800 (t0) cc_final: 0.8272 (t0) REVERT: C 146 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8030 (mtmp) REVERT: C 160 GLU cc_start: 0.8572 (tt0) cc_final: 0.8103 (mm-30) REVERT: C 184 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8174 (pt0) REVERT: C 201 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8351 (mp0) REVERT: C 208 LYS cc_start: 0.8650 (mtmm) cc_final: 0.8434 (mtmm) REVERT: C 281 GLN cc_start: 0.8715 (mm110) cc_final: 0.8183 (pt0) REVERT: C 402 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8377 (mt-10) REVERT: D 75 ASP cc_start: 0.8350 (t0) cc_final: 0.7694 (t0) REVERT: D 160 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8503 (mm-30) REVERT: D 184 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8155 (pt0) REVERT: D 199 LYS cc_start: 0.8314 (ptpt) cc_final: 0.8034 (ptmm) REVERT: D 201 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8400 (mp0) REVERT: D 206 ASP cc_start: 0.8440 (t0) cc_final: 0.8076 (t0) REVERT: D 208 LYS cc_start: 0.8674 (mtmm) cc_final: 0.8434 (mtmm) REVERT: D 272 TYR cc_start: 0.8881 (t80) cc_final: 0.7972 (t80) REVERT: D 281 GLN cc_start: 0.8645 (mm110) cc_final: 0.8200 (pt0) REVERT: D 283 LEU cc_start: 0.8696 (mt) cc_final: 0.8195 (mp) REVERT: D 402 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8288 (mt-10) REVERT: E 75 ASP cc_start: 0.8286 (t0) cc_final: 0.7920 (t0) REVERT: E 113 GLU cc_start: 0.9140 (mp0) cc_final: 0.8726 (mp0) REVERT: E 146 LYS cc_start: 0.8664 (mtpt) cc_final: 0.7976 (mtmp) REVERT: E 160 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8337 (mm-30) REVERT: E 201 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8313 (mp0) REVERT: E 206 ASP cc_start: 0.8373 (t0) cc_final: 0.8016 (t0) REVERT: E 208 LYS cc_start: 0.8527 (ptpt) cc_final: 0.8093 (mtmm) REVERT: E 227 LYS cc_start: 0.8754 (ptmt) cc_final: 0.8441 (ptpp) REVERT: E 232 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8352 (ttmm) REVERT: E 272 TYR cc_start: 0.8908 (t80) cc_final: 0.8230 (t80) REVERT: E 283 LEU cc_start: 0.8648 (mt) cc_final: 0.8162 (mp) outliers start: 44 outliers final: 23 residues processed: 364 average time/residue: 1.0118 time to fit residues: 407.8339 Evaluate side-chains 350 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 324 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 199 LYS 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 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 D residue 306 LEU Chi-restraints excluded: chain E residue 117 THR 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 207 LEU Chi-restraints excluded: chain E residue 233 SER 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: 0.9980 chunk 153 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 101 optimal weight: 0.0670 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- 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 ** 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 = 0.3157 r_free = 0.3157 target = 0.091531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.078000 restraints weight = 20556.827| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.55 r_work: 0.2815 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 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 = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13410 Z= 0.154 Angle : 0.546 9.457 18370 Z= 0.263 Chirality : 0.040 0.141 2235 Planarity : 0.004 0.037 2250 Dihedral : 4.337 36.565 2060 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.15 % Allowed : 19.86 % Favored : 76.99 % 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: 1.81 (0.21), residues: 1600 helix: 2.98 (0.20), residues: 525 sheet: 0.86 (0.25), residues: 430 loop : -0.04 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 112 HIS 0.002 0.000 HIS E 276 PHE 0.024 0.002 PHE C 297 TYR 0.024 0.002 TYR B 176 ARG 0.014 0.000 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 10) link_NAG-ASN : angle 1.21462 ( 30) link_BETA1-4 : bond 0.00200 ( 5) link_BETA1-4 : angle 1.28949 ( 15) hydrogen bonds : bond 0.03924 ( 680) hydrogen bonds : angle 4.08803 ( 2100) SS BOND : bond 0.00395 ( 10) SS BOND : angle 1.16898 ( 20) covalent geometry : bond 0.00343 (13385) covalent geometry : angle 0.54230 (18305) *********************** 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 379 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 334 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8594 (tp30) cc_final: 0.8155 (mm-30) REVERT: A 75 ASP cc_start: 0.8335 (t0) cc_final: 0.7942 (t0) REVERT: A 81 MET cc_start: 0.9055 (ttp) cc_final: 0.8720 (ptt) REVERT: A 132 ASP cc_start: 0.8389 (m-30) cc_final: 0.7941 (t0) REVERT: A 153 THR cc_start: 0.9323 (p) cc_final: 0.9038 (t) REVERT: A 201 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8373 (mp0) REVERT: A 206 ASP cc_start: 0.8455 (t0) cc_final: 0.8062 (t0) REVERT: A 208 LYS cc_start: 0.8546 (ptpt) cc_final: 0.8205 (mtmm) REVERT: A 232 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8239 (ttmm) REVERT: A 272 TYR cc_start: 0.8880 (t80) cc_final: 0.8239 (t80) REVERT: A 283 LEU cc_start: 0.8593 (mt) cc_final: 0.8270 (mp) REVERT: A 297 PHE cc_start: 0.8829 (m-80) cc_final: 0.8430 (m-10) REVERT: A 364 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8149 (mp0) REVERT: B 75 ASP cc_start: 0.8204 (t0) cc_final: 0.7708 (t0) REVERT: B 129 ASP cc_start: 0.8788 (t0) cc_final: 0.8279 (t0) REVERT: B 146 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8007 (mttp) REVERT: B 199 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7971 (ptmm) REVERT: B 201 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8262 (mp0) REVERT: B 206 ASP cc_start: 0.8376 (t0) cc_final: 0.7851 (t0) REVERT: B 260 GLU cc_start: 0.8854 (pm20) cc_final: 0.8365 (pm20) REVERT: B 281 GLN cc_start: 0.8678 (mm110) cc_final: 0.8298 (pt0) REVERT: C 75 ASP cc_start: 0.8342 (t0) cc_final: 0.8050 (t0) REVERT: C 113 GLU cc_start: 0.9136 (mp0) cc_final: 0.8752 (mp0) REVERT: C 129 ASP cc_start: 0.8794 (t0) cc_final: 0.8169 (t0) REVERT: C 146 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8009 (mtmp) REVERT: C 160 GLU cc_start: 0.8572 (tt0) cc_final: 0.8105 (mm-30) REVERT: C 184 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8120 (pt0) REVERT: C 201 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8398 (mp0) REVERT: C 208 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8330 (mtmm) REVERT: C 402 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8391 (mt-10) REVERT: D 48 GLU cc_start: 0.8586 (tp30) cc_final: 0.8271 (mm-30) REVERT: D 75 ASP cc_start: 0.8377 (t0) cc_final: 0.7827 (t0) REVERT: D 160 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8275 (tp30) REVERT: D 184 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8132 (pt0) REVERT: D 199 LYS cc_start: 0.8356 (ptpt) cc_final: 0.8047 (ptmm) REVERT: D 201 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8410 (mp0) REVERT: D 206 ASP cc_start: 0.8444 (t0) cc_final: 0.8058 (t0) REVERT: D 208 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8434 (mtmm) REVERT: D 272 TYR cc_start: 0.8913 (t80) cc_final: 0.8025 (t80) REVERT: D 281 GLN cc_start: 0.8669 (mm110) cc_final: 0.8201 (pt0) REVERT: D 283 LEU cc_start: 0.8731 (mt) cc_final: 0.8334 (mp) REVERT: D 402 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8310 (mt-10) REVERT: E 75 ASP cc_start: 0.8312 (t0) cc_final: 0.7961 (t0) REVERT: E 78 ARG cc_start: 0.8789 (mtp85) cc_final: 0.8498 (mtm110) REVERT: E 113 GLU cc_start: 0.9151 (mp0) cc_final: 0.8756 (mp0) REVERT: E 132 ASP cc_start: 0.7862 (t0) cc_final: 0.7597 (t0) REVERT: E 146 LYS cc_start: 0.8665 (mtpt) cc_final: 0.7986 (mtmp) REVERT: E 160 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8367 (mm-30) REVERT: E 201 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8364 (mp0) REVERT: E 206 ASP cc_start: 0.8400 (t0) cc_final: 0.8017 (t0) REVERT: E 208 LYS cc_start: 0.8530 (ptpt) cc_final: 0.8121 (mtmm) REVERT: E 283 LEU cc_start: 0.8575 (mt) cc_final: 0.8260 (mp) outliers start: 45 outliers final: 24 residues processed: 360 average time/residue: 1.0380 time to fit residues: 412.2998 Evaluate side-chains 352 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 324 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 199 LYS 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 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 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 117 THR 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 277 SER Chi-restraints excluded: chain E residue 305 PHE 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: 4.9990 chunk 23 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 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 = 0.3134 r_free = 0.3134 target = 0.090141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.076624 restraints weight = 20438.865| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.50 r_work: 0.2774 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 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 = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13410 Z= 0.205 Angle : 0.578 9.592 18370 Z= 0.279 Chirality : 0.041 0.161 2235 Planarity : 0.004 0.032 2250 Dihedral : 4.284 31.038 2060 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.08 % Allowed : 19.93 % Favored : 76.99 % 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: 1.71 (0.21), residues: 1600 helix: 2.78 (0.20), residues: 530 sheet: 0.79 (0.25), residues: 430 loop : 0.01 (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 103 PHE 0.026 0.002 PHE C 297 TYR 0.037 0.003 TYR B 176 ARG 0.010 0.000 ARG E 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 10) link_NAG-ASN : angle 1.29274 ( 30) link_BETA1-4 : bond 0.00149 ( 5) link_BETA1-4 : angle 1.27254 ( 15) hydrogen bonds : bond 0.04045 ( 680) hydrogen bonds : angle 4.15211 ( 2100) SS BOND : bond 0.00471 ( 10) SS BOND : angle 1.28150 ( 20) covalent geometry : bond 0.00464 (13385) covalent geometry : angle 0.57394 (18305) *********************** 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 368 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 324 time to evaluate : 1.360 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: 0.8586 (tp30) cc_final: 0.8139 (mm-30) REVERT: A 75 ASP cc_start: 0.8322 (t0) cc_final: 0.7916 (t0) REVERT: A 81 MET cc_start: 0.9067 (ttp) cc_final: 0.8754 (ptt) REVERT: A 153 THR cc_start: 0.9333 (p) cc_final: 0.9033 (t) REVERT: A 184 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8397 (mt-10) REVERT: A 201 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8397 (mp0) REVERT: A 206 ASP cc_start: 0.8460 (t0) cc_final: 0.8082 (t0) REVERT: A 208 LYS cc_start: 0.8550 (ptpt) cc_final: 0.8193 (mtmm) REVERT: A 272 TYR cc_start: 0.8908 (t80) cc_final: 0.8284 (t80) REVERT: A 283 LEU cc_start: 0.8613 (mt) cc_final: 0.8311 (mp) REVERT: A 297 PHE cc_start: 0.8853 (m-80) cc_final: 0.8485 (m-10) REVERT: A 364 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8157 (mp0) REVERT: B 75 ASP cc_start: 0.8211 (t0) cc_final: 0.7715 (t0) REVERT: B 129 ASP cc_start: 0.8807 (t0) cc_final: 0.8265 (t0) REVERT: B 146 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8430 (mtmt) REVERT: B 199 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7967 (ptmm) REVERT: B 201 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8268 (mp0) REVERT: B 206 ASP cc_start: 0.8350 (t0) cc_final: 0.7862 (t0) REVERT: B 260 GLU cc_start: 0.8852 (pm20) cc_final: 0.8325 (pm20) REVERT: C 75 ASP cc_start: 0.8354 (t0) cc_final: 0.8009 (t0) REVERT: C 113 GLU cc_start: 0.9127 (mp0) cc_final: 0.8766 (mp0) REVERT: C 129 ASP cc_start: 0.8791 (t0) cc_final: 0.8221 (t0) REVERT: C 146 LYS cc_start: 0.8635 (mtpt) cc_final: 0.8005 (mtmp) REVERT: C 160 GLU cc_start: 0.8582 (tt0) cc_final: 0.8115 (mm-30) REVERT: C 184 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8221 (pt0) REVERT: C 199 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7820 (ptmm) REVERT: C 201 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8453 (mp0) REVERT: C 402 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8406 (mt-10) REVERT: D 75 ASP cc_start: 0.8390 (t0) cc_final: 0.7806 (t0) REVERT: D 146 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8040 (mttp) REVERT: D 160 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8498 (mm-30) REVERT: D 184 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8124 (pt0) REVERT: D 199 LYS cc_start: 0.8440 (ptpt) cc_final: 0.8107 (ptmm) REVERT: D 201 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8420 (mp0) REVERT: D 206 ASP cc_start: 0.8470 (t0) cc_final: 0.8074 (t0) REVERT: D 208 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8413 (mtmm) REVERT: D 272 TYR cc_start: 0.8962 (t80) cc_final: 0.8073 (t80) REVERT: D 281 GLN cc_start: 0.8692 (mm110) cc_final: 0.8252 (pt0) REVERT: D 283 LEU cc_start: 0.8651 (mt) cc_final: 0.8131 (mp) REVERT: D 402 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8291 (mt-10) REVERT: E 75 ASP cc_start: 0.8317 (t0) cc_final: 0.7941 (t0) REVERT: E 113 GLU cc_start: 0.9168 (mp0) cc_final: 0.8883 (mp0) REVERT: E 132 ASP cc_start: 0.7888 (t0) cc_final: 0.7585 (t0) REVERT: E 146 LYS cc_start: 0.8670 (mtpt) cc_final: 0.7995 (mtmp) REVERT: E 160 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8385 (mm-30) REVERT: E 167 ASP cc_start: 0.9418 (p0) cc_final: 0.9071 (p0) REVERT: E 201 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8360 (mp0) REVERT: E 206 ASP cc_start: 0.8432 (t0) cc_final: 0.8137 (t0) REVERT: E 232 LYS cc_start: 0.8726 (ttmt) cc_final: 0.8356 (ttmm) REVERT: E 283 LEU cc_start: 0.8676 (mt) cc_final: 0.8388 (mp) outliers start: 44 outliers final: 22 residues processed: 352 average time/residue: 1.0309 time to fit residues: 400.8925 Evaluate side-chains 339 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 312 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 199 LYS 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 B residue 277 SER 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 277 SER Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 85 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 155 THR Chi-restraints excluded: chain E residue 160 GLU 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: 4.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 C 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 = 0.3149 r_free = 0.3149 target = 0.090914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.077663 restraints weight = 20602.336| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.44 r_work: 0.2790 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13410 Z= 0.178 Angle : 0.587 11.078 18370 Z= 0.284 Chirality : 0.042 0.477 2235 Planarity : 0.004 0.032 2250 Dihedral : 4.224 26.020 2060 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.45 % Allowed : 20.91 % 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: 1.69 (0.21), residues: 1600 helix: 2.84 (0.20), residues: 525 sheet: 0.79 (0.25), residues: 430 loop : -0.07 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 112 HIS 0.002 0.000 HIS B 276 PHE 0.026 0.002 PHE C 297 TYR 0.050 0.003 TYR D 176 ARG 0.011 0.001 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 10) link_NAG-ASN : angle 1.24747 ( 30) link_BETA1-4 : bond 0.00157 ( 5) link_BETA1-4 : angle 1.23166 ( 15) hydrogen bonds : bond 0.04048 ( 680) hydrogen bonds : angle 4.16589 ( 2100) SS BOND : bond 0.00423 ( 10) SS BOND : angle 1.23078 ( 20) covalent geometry : bond 0.00400 (13385) covalent geometry : angle 0.58377 (18305) ********************** 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 347 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 312 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8634 (tp30) cc_final: 0.8197 (mm-30) REVERT: A 75 ASP cc_start: 0.8402 (t0) cc_final: 0.8026 (t0) REVERT: A 81 MET cc_start: 0.9078 (ttp) cc_final: 0.8812 (ptt) REVERT: A 153 THR cc_start: 0.9344 (p) cc_final: 0.9063 (t) REVERT: A 201 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8457 (mp0) REVERT: A 206 ASP cc_start: 0.8480 (t0) cc_final: 0.8148 (t0) REVERT: A 208 LYS cc_start: 0.8620 (ptpt) cc_final: 0.8276 (mtmm) REVERT: A 272 TYR cc_start: 0.8950 (t80) cc_final: 0.8348 (t80) REVERT: A 283 LEU cc_start: 0.8583 (mt) cc_final: 0.8240 (mp) REVERT: A 297 PHE cc_start: 0.8905 (m-80) cc_final: 0.8546 (m-10) REVERT: A 364 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8232 (mp0) REVERT: B 75 ASP cc_start: 0.8270 (t0) cc_final: 0.7792 (t0) REVERT: B 129 ASP cc_start: 0.8814 (t0) cc_final: 0.8284 (t0) REVERT: B 146 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8137 (mttp) REVERT: B 199 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8019 (ptmm) REVERT: B 201 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8310 (mp0) REVERT: B 206 ASP cc_start: 0.8357 (t0) cc_final: 0.7898 (t0) REVERT: B 260 GLU cc_start: 0.8864 (pm20) cc_final: 0.8350 (pm20) REVERT: C 75 ASP cc_start: 0.8428 (t0) cc_final: 0.8125 (t0) REVERT: C 113 GLU cc_start: 0.9106 (mp0) cc_final: 0.8791 (mp0) REVERT: C 129 ASP cc_start: 0.8837 (t0) cc_final: 0.8256 (t0) REVERT: C 146 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8111 (mtmp) REVERT: C 160 GLU cc_start: 0.8591 (tt0) cc_final: 0.8168 (mm-30) REVERT: C 184 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8282 (pt0) REVERT: C 201 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8523 (mp0) REVERT: C 402 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8455 (mt-10) REVERT: D 75 ASP cc_start: 0.8463 (t0) cc_final: 0.7905 (t0) REVERT: D 146 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8109 (mttp) REVERT: D 160 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8566 (mm-30) REVERT: D 184 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8198 (pt0) REVERT: D 199 LYS cc_start: 0.8468 (ptpt) cc_final: 0.8151 (ptmm) REVERT: D 201 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8478 (mp0) REVERT: D 206 ASP cc_start: 0.8477 (t0) cc_final: 0.8109 (t0) REVERT: D 208 LYS cc_start: 0.8709 (mtmm) cc_final: 0.8459 (mtmm) REVERT: D 272 TYR cc_start: 0.8981 (t80) cc_final: 0.8109 (t80) REVERT: D 281 GLN cc_start: 0.8685 (mm110) cc_final: 0.8260 (pt0) REVERT: D 283 LEU cc_start: 0.8646 (mt) cc_final: 0.8145 (mp) REVERT: D 402 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8358 (mt-10) REVERT: E 75 ASP cc_start: 0.8374 (t0) cc_final: 0.8046 (t0) REVERT: E 113 GLU cc_start: 0.9139 (mp0) cc_final: 0.8901 (mp0) REVERT: E 132 ASP cc_start: 0.7849 (t0) cc_final: 0.7565 (t0) REVERT: E 146 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8085 (mtmp) REVERT: E 160 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8416 (mm-30) REVERT: E 167 ASP cc_start: 0.9429 (p0) cc_final: 0.9084 (p0) REVERT: E 201 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8415 (mp0) REVERT: E 206 ASP cc_start: 0.8453 (t0) cc_final: 0.8104 (t0) REVERT: E 208 LYS cc_start: 0.8757 (mtmm) cc_final: 0.8236 (mtmm) REVERT: E 232 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8422 (ttmm) REVERT: E 272 TYR cc_start: 0.8969 (t80) cc_final: 0.8223 (t80) REVERT: E 283 LEU cc_start: 0.8669 (mt) cc_final: 0.8424 (mp) outliers start: 35 outliers final: 27 residues processed: 334 average time/residue: 1.0242 time to fit residues: 377.5923 Evaluate side-chains 332 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 146 LYS Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 199 LYS 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 B residue 277 SER Chi-restraints excluded: chain C residue 123 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 277 SER Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 85 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 306 LEU 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 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 74 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 382 GLN C 156 ASN C 221 GLN D 221 GLN D 382 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.090842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.077549 restraints weight = 20568.051| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.44 r_work: 0.2785 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 13410 Z= 0.231 Angle : 0.824 59.198 18370 Z= 0.457 Chirality : 0.046 0.817 2235 Planarity : 0.004 0.042 2250 Dihedral : 4.246 26.244 2060 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.38 % Allowed : 21.33 % Favored : 76.29 % Cbeta Deviations : 0.06 % 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: 1.67 (0.21), residues: 1600 helix: 2.82 (0.20), residues: 525 sheet: 0.79 (0.25), residues: 430 loop : -0.08 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 112 HIS 0.002 0.000 HIS B 276 PHE 0.024 0.002 PHE A 385 TYR 0.040 0.002 TYR D 176 ARG 0.012 0.001 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 10) link_NAG-ASN : angle 1.23571 ( 30) link_BETA1-4 : bond 0.00244 ( 5) link_BETA1-4 : angle 1.37645 ( 15) hydrogen bonds : bond 0.04059 ( 680) hydrogen bonds : angle 4.16802 ( 2100) SS BOND : bond 0.00651 ( 10) SS BOND : angle 1.14462 ( 20) covalent geometry : bond 0.00541 (13385) covalent geometry : angle 0.82184 (18305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9402.08 seconds wall clock time: 162 minutes 20.03 seconds (9740.03 seconds total)