Starting phenix.real_space_refine on Sun May 3 12:00:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9let_63033/05_2026/9let_63033.cif Found real_map, /net/cci-nas-00/data/ceres_data/9let_63033/05_2026/9let_63033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9let_63033/05_2026/9let_63033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9let_63033/05_2026/9let_63033.map" model { file = "/net/cci-nas-00/data/ceres_data/9let_63033/05_2026/9let_63033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9let_63033/05_2026/9let_63033.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 5 6.06 5 S 55 5.16 5 C 8285 2.51 5 N 2070 2.21 5 O 2330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12745 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2470 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.30, per 1000 atoms: 0.26 Number of scatterers: 12745 At special positions: 0 Unit cell: (97.86, 97.86, 124.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 5 29.99 S 55 16.00 O 2330 8.00 N 2070 7.00 C 8285 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=2.01 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 E 157 " - pdb=" SG CYS E 171 " distance=2.05 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 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 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 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 F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 170 " " NAG H 1 " - " ASN B 55 " " NAG I 1 " - " ASN B 170 " " NAG J 1 " - " ASN E 55 " " NAG K 1 " - " ASN E 170 " " NAG L 1 " - " ASN D 55 " " NAG M 1 " - " ASN D 170 " " NAG N 1 " - " ASN C 55 " " NAG O 1 " - " ASN C 170 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 566.8 milliseconds 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3020 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 20 sheets defined 35.9% alpha, 38.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.657A 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 282 removed outlier: 4.200A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 322 removed outlier: 3.948A pdb=" N TYR A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 391 Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 231 through 252 removed outlier: 4.656A 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 281 removed outlier: 4.284A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 322 removed outlier: 4.041A pdb=" N TYR B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 391 Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 231 through 252 removed outlier: 4.657A 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 282 removed outlier: 4.284A pdb=" N GLY E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 322 removed outlier: 4.042A pdb=" N TYR E 295 " --> pdb=" O PRO E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 391 Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 231 through 252 removed outlier: 4.657A 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 282 removed outlier: 4.284A pdb=" N GLY D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 322 removed outlier: 4.042A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 391 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 231 through 252 removed outlier: 4.656A 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 282 removed outlier: 4.284A pdb=" N GLY C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 322 removed outlier: 4.041A pdb=" N TYR C 295 " --> pdb=" O PRO C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 391 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 6.211A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA A 150 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP A 130 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR A 152 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL A 128 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.765A 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: 6.211A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR A 80 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL A 74 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU A 86 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL A 68 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG A 88 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL A 66 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER A 90 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL A 64 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N LEU A 92 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL A 62 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 68 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111 removed outlier: 6.210A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA B 150 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TRP B 130 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR B 152 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL B 128 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU B 154 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 111 removed outlier: 6.210A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR B 80 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL B 74 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU B 86 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL B 68 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG B 88 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL B 66 " --> pdb=" O ARG B 88 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N SER B 90 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL B 64 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N LEU B 92 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL B 62 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 68 " --> pdb=" O VAL B 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 122 Processing sheet with id=AA8, first strand: chain 'B' and resid 121 through 122 Processing sheet with id=AA9, first strand: chain 'E' and resid 107 through 111 removed outlier: 6.211A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA E 150 " --> pdb=" O TRP E 130 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP E 130 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR E 152 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL E 128 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU E 154 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 107 through 111 removed outlier: 6.211A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR E 80 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL E 74 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU E 86 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL E 68 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG E 88 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL E 66 " --> pdb=" O ARG E 88 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER E 90 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL E 64 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N LEU E 92 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL E 62 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL E 68 " --> pdb=" O VAL E 192 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 121 through 122 Processing sheet with id=AB3, first strand: chain 'E' and resid 121 through 122 Processing sheet with id=AB4, first strand: chain 'D' and resid 107 through 111 removed outlier: 6.211A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA D 150 " --> pdb=" O TRP D 130 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TRP D 130 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR D 152 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL D 128 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU D 154 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 107 through 111 removed outlier: 6.211A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR D 80 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL D 74 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU D 86 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL D 68 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ARG D 88 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL D 66 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N SER D 90 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL D 64 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N LEU D 92 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL D 62 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL D 68 " --> pdb=" O VAL D 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 121 through 122 Processing sheet with id=AB7, first strand: chain 'D' and resid 121 through 122 Processing sheet with id=AB8, first strand: chain 'C' and resid 107 through 111 removed outlier: 6.210A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA C 150 " --> pdb=" O TRP C 130 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP C 130 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR C 152 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL C 128 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU C 154 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 107 through 111 removed outlier: 6.210A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR C 80 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL C 74 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU C 86 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL C 68 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG C 88 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL C 66 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N SER C 90 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL C 64 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N LEU C 92 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL C 62 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 68 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AC2, first strand: chain 'C' and resid 121 through 122 754 hydrogen bonds defined for protein. 2202 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1946 1.30 - 1.43: 3434 1.43 - 1.56: 7584 1.56 - 1.69: 1 1.69 - 1.82: 75 Bond restraints: 13040 Sorted by residual: bond pdb=" C ARG A 65 " pdb=" O ARG A 65 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.14e-02 7.69e+03 3.36e+01 bond pdb=" C ARG B 65 " pdb=" O ARG B 65 " ideal model delta sigma weight residual 1.236 1.171 0.065 1.14e-02 7.69e+03 3.23e+01 bond pdb=" C VAL C 66 " pdb=" O VAL C 66 " ideal model delta sigma weight residual 1.238 1.172 0.066 1.17e-02 7.31e+03 3.17e+01 bond pdb=" CA ALA D 107 " pdb=" C ALA D 107 " ideal model delta sigma weight residual 1.521 1.452 0.069 1.28e-02 6.10e+03 2.91e+01 bond pdb=" C VAL A 64 " pdb=" O VAL A 64 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.13e-02 7.83e+03 2.90e+01 ... (remaining 13035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 17211 2.24 - 4.48: 533 4.48 - 6.72: 90 6.72 - 8.96: 13 8.96 - 11.20: 3 Bond angle restraints: 17850 Sorted by residual: angle pdb=" N ASN B 55 " pdb=" CA ASN B 55 " pdb=" C ASN B 55 " ideal model delta sigma weight residual 112.30 103.12 9.18 1.36e+00 5.41e-01 4.55e+01 angle pdb=" N SER A 197 " pdb=" CA SER A 197 " pdb=" C SER A 197 " ideal model delta sigma weight residual 108.23 119.43 -11.20 1.72e+00 3.38e-01 4.24e+01 angle pdb=" N ASN D 55 " pdb=" CA ASN D 55 " pdb=" C ASN D 55 " ideal model delta sigma weight residual 110.88 103.50 7.38 1.28e+00 6.10e-01 3.32e+01 angle pdb=" N PHE E 159 " pdb=" CA PHE E 159 " pdb=" C PHE E 159 " ideal model delta sigma weight residual 109.59 117.94 -8.35 1.47e+00 4.63e-01 3.23e+01 angle pdb=" CA ASN D 73 " pdb=" C ASN D 73 " pdb=" N VAL D 74 " ideal model delta sigma weight residual 115.51 122.78 -7.27 1.30e+00 5.92e-01 3.13e+01 ... (remaining 17845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.12: 7655 23.12 - 46.23: 322 46.23 - 69.35: 40 69.35 - 92.47: 66 92.47 - 115.58: 42 Dihedral angle restraints: 8125 sinusoidal: 3515 harmonic: 4610 Sorted by residual: dihedral pdb=" CB CYS A 289 " pdb=" SG CYS A 289 " pdb=" SG CYS A 394 " pdb=" CB CYS A 394 " ideal model delta sinusoidal sigma weight residual 93.00 143.68 -50.68 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" C3 BMA L 3 " pdb=" C1 BMA L 3 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " ideal model delta sinusoidal sigma weight residual -63.01 52.57 -115.58 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" O2 BMA L 3 " pdb=" C1 BMA L 3 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " ideal model delta sinusoidal sigma weight residual 60.15 174.04 -113.89 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 8122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2095 0.112 - 0.224: 125 0.224 - 0.336: 26 0.336 - 0.448: 4 0.448 - 0.560: 5 Chirality restraints: 2255 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.89e+01 chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.20e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.46e+01 ... (remaining 2252 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " 0.294 2.00e-02 2.50e+03 2.54e-01 8.08e+02 pdb=" C7 NAG K 1 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " 0.001 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " -0.436 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.284 2.00e-02 2.50e+03 2.40e-01 7.19e+02 pdb=" C7 NAG I 1 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.410 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.220 2.00e-02 2.50e+03 1.88e-01 4.42e+02 pdb=" C7 NAG G 1 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.309 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.171 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1432 2.75 - 3.29: 12046 3.29 - 3.83: 21939 3.83 - 4.36: 25955 4.36 - 4.90: 44726 Nonbonded interactions: 106098 Sorted by model distance: nonbonded pdb=" OD2 ASP A 142 " pdb=" ND1 HIS A 144 " model vdw 2.213 3.120 nonbonded pdb=" OE2 GLU E 242 " pdb=" OH TYR E 296 " model vdw 2.248 3.040 nonbonded pdb=" OE2 GLU B 242 " pdb=" OH TYR B 296 " model vdw 2.248 3.040 nonbonded pdb=" OE2 GLU D 242 " pdb=" OH TYR D 296 " model vdw 2.248 3.040 nonbonded pdb=" OE2 GLU A 242 " pdb=" OH TYR A 296 " model vdw 2.248 3.040 ... (remaining 106093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 47 through 395) selection = (chain 'B' and resid 47 through 395) selection = (chain 'C' and resid 47 through 395) selection = (chain 'D' and resid 47 through 395) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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=1.00 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: 1.640 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.950 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 0.069 13080 Z= 0.471 Angle : 0.923 11.199 17960 Z= 0.527 Chirality : 0.066 0.560 2255 Planarity : 0.012 0.254 2150 Dihedral : 17.759 115.584 5075 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.22), residues: 1535 helix: 2.40 (0.21), residues: 495 sheet: 1.23 (0.25), residues: 465 loop : -0.22 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 105 TYR 0.012 0.001 TYR A 272 PHE 0.014 0.002 PHE A 159 TRP 0.013 0.001 TRP E 112 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00706 (13040) covalent geometry : angle 0.89554 (17850) SS BOND : bond 0.00909 ( 10) SS BOND : angle 1.82804 ( 20) hydrogen bonds : bond 0.13525 ( 669) hydrogen bonds : angle 6.51033 ( 2202) link_BETA1-4 : bond 0.00887 ( 20) link_BETA1-4 : angle 2.58124 ( 60) link_NAG-ASN : bond 0.01687 ( 10) link_NAG-ASN : angle 4.18135 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.465 Fit side-chains REVERT: A 146 LYS cc_start: 0.7809 (mttm) cc_final: 0.7604 (mtmm) REVERT: A 208 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8156 (mttp) REVERT: C 49 SER cc_start: 0.7491 (m) cc_final: 0.7207 (p) REVERT: C 369 ILE cc_start: 0.8709 (mt) cc_final: 0.8427 (mm) outliers start: 0 outliers final: 2 residues processed: 350 average time/residue: 0.5902 time to fit residues: 224.1548 Evaluate side-chains 251 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 249 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain D residue 235 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 73 ASN A 156 ASN A 158 ASN A 180 ASN A 188 GLN A 215 GLN A 221 GLN A 382 GLN B 141 GLN B 215 GLN B 221 GLN E 180 ASN E 215 GLN E 382 GLN D 51 GLN D 148 ASN D 180 ASN D 215 GLN D 382 GLN C 180 ASN C 382 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123678 restraints weight = 12136.739| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.90 r_work: 0.3274 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13080 Z= 0.151 Angle : 0.626 7.268 17960 Z= 0.304 Chirality : 0.042 0.146 2255 Planarity : 0.004 0.045 2150 Dihedral : 12.108 102.398 2279 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.68 % Allowed : 11.19 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.22), residues: 1535 helix: 2.81 (0.21), residues: 495 sheet: 1.35 (0.25), residues: 465 loop : -0.10 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 78 TYR 0.014 0.002 TYR E 272 PHE 0.015 0.002 PHE E 175 TRP 0.010 0.002 TRP E 389 HIS 0.004 0.001 HIS B 276 Details of bonding type rmsd covalent geometry : bond 0.00330 (13040) covalent geometry : angle 0.60818 (17850) SS BOND : bond 0.00609 ( 10) SS BOND : angle 0.89569 ( 20) hydrogen bonds : bond 0.04604 ( 669) hydrogen bonds : angle 4.66135 ( 2202) link_BETA1-4 : bond 0.00562 ( 20) link_BETA1-4 : angle 2.34843 ( 60) link_NAG-ASN : bond 0.00317 ( 10) link_NAG-ASN : angle 1.81886 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 274 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 135 PRO cc_start: 0.8176 (Cg_endo) cc_final: 0.7765 (Cg_exo) REVERT: A 146 LYS cc_start: 0.8307 (mttm) cc_final: 0.7690 (mtmm) REVERT: A 201 GLU cc_start: 0.7896 (tt0) cc_final: 0.7679 (tt0) REVERT: A 208 LYS cc_start: 0.8404 (mtmt) cc_final: 0.7820 (mttp) REVERT: B 49 SER cc_start: 0.7429 (m) cc_final: 0.7199 (p) REVERT: B 259 ILE cc_start: 0.7897 (mm) cc_final: 0.7568 (pt) REVERT: B 372 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7886 (mm) REVERT: E 148 ASN cc_start: 0.8146 (OUTLIER) cc_final: 0.7449 (p0) REVERT: E 188 GLN cc_start: 0.8568 (tt0) cc_final: 0.8364 (tt0) REVERT: E 381 THR cc_start: 0.8241 (t) cc_final: 0.7811 (p) REVERT: D 167 ASP cc_start: 0.8369 (p0) cc_final: 0.8099 (p0) REVERT: C 54 ASN cc_start: 0.7502 (OUTLIER) cc_final: 0.7154 (t0) REVERT: C 113 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: C 142 ASP cc_start: 0.6653 (p0) cc_final: 0.6326 (p0) REVERT: C 369 ILE cc_start: 0.8463 (mt) cc_final: 0.8048 (mm) outliers start: 51 outliers final: 28 residues processed: 299 average time/residue: 0.5886 time to fit residues: 191.1615 Evaluate side-chains 280 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 0.0060 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 0.0970 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 188 GLN B 141 GLN D 51 GLN D 73 ASN D 382 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123607 restraints weight = 11918.840| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.83 r_work: 0.3248 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13080 Z= 0.160 Angle : 0.594 6.182 17960 Z= 0.292 Chirality : 0.042 0.141 2255 Planarity : 0.004 0.039 2150 Dihedral : 8.176 95.624 2277 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.55 % Allowed : 12.92 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.21), residues: 1535 helix: 3.14 (0.21), residues: 485 sheet: 1.43 (0.28), residues: 370 loop : -0.19 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 88 TYR 0.017 0.002 TYR B 296 PHE 0.014 0.002 PHE B 220 TRP 0.017 0.002 TRP E 389 HIS 0.004 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00364 (13040) covalent geometry : angle 0.57859 (17850) SS BOND : bond 0.00181 ( 10) SS BOND : angle 0.94868 ( 20) hydrogen bonds : bond 0.04716 ( 669) hydrogen bonds : angle 4.43368 ( 2202) link_BETA1-4 : bond 0.00574 ( 20) link_BETA1-4 : angle 2.14267 ( 60) link_NAG-ASN : bond 0.00280 ( 10) link_NAG-ASN : angle 1.57117 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 262 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 146 LYS cc_start: 0.8433 (mttm) cc_final: 0.7901 (mtmm) REVERT: A 208 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8026 (mttp) REVERT: A 210 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7639 (pt0) REVERT: A 390 MET cc_start: 0.7481 (mtp) cc_final: 0.6498 (mpt) REVERT: B 49 SER cc_start: 0.7603 (m) cc_final: 0.7304 (p) REVERT: B 85 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8107 (mp) REVERT: B 208 LYS cc_start: 0.7146 (mtmt) cc_final: 0.6798 (mttp) REVERT: B 257 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7293 (ptt180) REVERT: B 259 ILE cc_start: 0.8027 (mm) cc_final: 0.7801 (pt) REVERT: E 188 GLN cc_start: 0.8653 (tt0) cc_final: 0.8424 (tt0) REVERT: E 381 THR cc_start: 0.8298 (t) cc_final: 0.8000 (p) REVERT: D 167 ASP cc_start: 0.8525 (p0) cc_final: 0.8076 (p0) REVERT: C 113 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: C 369 ILE cc_start: 0.8617 (mt) cc_final: 0.8194 (mm) outliers start: 63 outliers final: 34 residues processed: 299 average time/residue: 0.5823 time to fit residues: 189.3479 Evaluate side-chains 280 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 242 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 286 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 102 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 39 optimal weight: 0.1980 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 290 ASN B 141 GLN B 382 GLN E 156 ASN E 188 GLN D 51 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.148830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121490 restraints weight = 11746.466| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.86 r_work: 0.3212 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13080 Z= 0.168 Angle : 0.585 7.108 17960 Z= 0.289 Chirality : 0.041 0.165 2255 Planarity : 0.004 0.040 2150 Dihedral : 6.845 88.843 2275 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.49 % Allowed : 14.30 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.21), residues: 1535 helix: 3.20 (0.21), residues: 480 sheet: 0.90 (0.26), residues: 415 loop : -0.18 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 88 TYR 0.019 0.002 TYR A 176 PHE 0.014 0.002 PHE E 164 TRP 0.014 0.002 TRP C 389 HIS 0.004 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00382 (13040) covalent geometry : angle 0.57144 (17850) SS BOND : bond 0.00185 ( 10) SS BOND : angle 1.00791 ( 20) hydrogen bonds : bond 0.04649 ( 669) hydrogen bonds : angle 4.37284 ( 2202) link_BETA1-4 : bond 0.00465 ( 20) link_BETA1-4 : angle 1.94885 ( 60) link_NAG-ASN : bond 0.00216 ( 10) link_NAG-ASN : angle 1.51546 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 242 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 146 LYS cc_start: 0.8417 (mttm) cc_final: 0.7842 (mtmm) REVERT: A 208 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8062 (mttp) REVERT: A 210 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: B 49 SER cc_start: 0.7731 (m) cc_final: 0.7410 (p) REVERT: B 85 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8154 (mt) REVERT: B 208 LYS cc_start: 0.7539 (mtmt) cc_final: 0.6923 (mttp) REVERT: B 257 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7313 (ptt180) REVERT: B 368 ARG cc_start: 0.7062 (mtm110) cc_final: 0.6769 (mtm-85) REVERT: E 381 THR cc_start: 0.8370 (t) cc_final: 0.8123 (p) REVERT: D 86 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8550 (tt) REVERT: D 88 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7250 (ttt90) REVERT: D 167 ASP cc_start: 0.8596 (p0) cc_final: 0.8119 (p0) REVERT: C 54 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7407 (t0) REVERT: C 113 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: C 160 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: C 201 GLU cc_start: 0.8112 (tt0) cc_final: 0.7542 (tt0) REVERT: C 369 ILE cc_start: 0.8585 (mt) cc_final: 0.8185 (mm) outliers start: 76 outliers final: 45 residues processed: 282 average time/residue: 0.5596 time to fit residues: 171.6229 Evaluate side-chains 290 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 47 optimal weight: 0.0870 chunk 87 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 GLN B 190 HIS D 47 GLN D 51 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123630 restraints weight = 11891.808| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.89 r_work: 0.3242 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13080 Z= 0.119 Angle : 0.530 7.248 17960 Z= 0.261 Chirality : 0.039 0.133 2255 Planarity : 0.004 0.042 2150 Dihedral : 6.420 81.112 2275 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.48 % Allowed : 16.03 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.22), residues: 1535 helix: 3.34 (0.21), residues: 480 sheet: 0.82 (0.26), residues: 415 loop : -0.10 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 88 TYR 0.020 0.002 TYR A 176 PHE 0.013 0.001 PHE B 220 TRP 0.011 0.001 TRP C 389 HIS 0.002 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00255 (13040) covalent geometry : angle 0.51754 (17850) SS BOND : bond 0.00178 ( 10) SS BOND : angle 0.65733 ( 20) hydrogen bonds : bond 0.04296 ( 669) hydrogen bonds : angle 4.16002 ( 2202) link_BETA1-4 : bond 0.00464 ( 20) link_BETA1-4 : angle 1.76965 ( 60) link_NAG-ASN : bond 0.00121 ( 10) link_NAG-ASN : angle 1.40193 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 263 time to evaluate : 0.484 Fit side-chains REVERT: A 47 GLN cc_start: 0.5379 (tt0) cc_final: 0.5035 (tp-100) REVERT: A 146 LYS cc_start: 0.8358 (mttm) cc_final: 0.7802 (mttp) REVERT: A 208 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8100 (mttp) REVERT: B 49 SER cc_start: 0.7754 (m) cc_final: 0.7424 (p) REVERT: B 85 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8072 (mt) REVERT: B 208 LYS cc_start: 0.7635 (mtmt) cc_final: 0.7103 (mttp) REVERT: B 257 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7323 (ptt180) REVERT: B 368 ARG cc_start: 0.7059 (mtm110) cc_final: 0.6790 (mtm-85) REVERT: D 47 GLN cc_start: 0.5078 (tt0) cc_final: 0.4851 (tt0) REVERT: D 86 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8570 (tt) REVERT: D 109 THR cc_start: 0.8376 (p) cc_final: 0.8155 (t) REVERT: D 368 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7374 (mtp180) REVERT: C 113 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: C 369 ILE cc_start: 0.8629 (mt) cc_final: 0.8190 (mm) outliers start: 62 outliers final: 44 residues processed: 295 average time/residue: 0.5638 time to fit residues: 180.6002 Evaluate side-chains 294 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN B 141 GLN D 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.147208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.119871 restraints weight = 11886.342| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.88 r_work: 0.3213 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13080 Z= 0.168 Angle : 0.584 7.071 17960 Z= 0.288 Chirality : 0.041 0.206 2255 Planarity : 0.004 0.057 2150 Dihedral : 6.276 75.241 2275 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.27 % Allowed : 16.03 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.22), residues: 1535 helix: 3.21 (0.21), residues: 480 sheet: 0.65 (0.26), residues: 415 loop : -0.06 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 88 TYR 0.021 0.002 TYR A 176 PHE 0.016 0.002 PHE E 385 TRP 0.012 0.001 TRP C 389 HIS 0.005 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00386 (13040) covalent geometry : angle 0.57279 (17850) SS BOND : bond 0.00286 ( 10) SS BOND : angle 0.95041 ( 20) hydrogen bonds : bond 0.04571 ( 669) hydrogen bonds : angle 4.23876 ( 2202) link_BETA1-4 : bond 0.00449 ( 20) link_BETA1-4 : angle 1.81887 ( 60) link_NAG-ASN : bond 0.00191 ( 10) link_NAG-ASN : angle 1.42334 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 256 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.5409 (tt0) cc_final: 0.5065 (tp-100) REVERT: A 106 HIS cc_start: 0.7371 (m170) cc_final: 0.6930 (m170) REVERT: A 146 LYS cc_start: 0.8401 (mttm) cc_final: 0.7835 (mtmm) REVERT: A 208 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8111 (mttp) REVERT: A 210 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7605 (pt0) REVERT: B 49 SER cc_start: 0.7796 (m) cc_final: 0.7454 (p) REVERT: B 85 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8145 (mp) REVERT: B 208 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7253 (mttp) REVERT: B 227 LYS cc_start: 0.8759 (ptpt) cc_final: 0.8437 (ptmm) REVERT: B 257 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7317 (ptt180) REVERT: B 368 ARG cc_start: 0.7096 (mtm110) cc_final: 0.6831 (mtm-85) REVERT: D 47 GLN cc_start: 0.5080 (tt0) cc_final: 0.4747 (tt0) REVERT: D 86 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8560 (tt) REVERT: D 88 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7263 (ttt90) REVERT: D 167 ASP cc_start: 0.8578 (p0) cc_final: 0.8108 (p0) REVERT: D 368 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7429 (mtp180) REVERT: C 54 ASN cc_start: 0.7706 (OUTLIER) cc_final: 0.7374 (t0) REVERT: C 113 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: C 160 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: C 369 ILE cc_start: 0.8609 (mt) cc_final: 0.8198 (mm) outliers start: 73 outliers final: 54 residues processed: 292 average time/residue: 0.5836 time to fit residues: 185.2799 Evaluate side-chains 320 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 258 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 36 optimal weight: 0.0670 chunk 84 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 overall best weight: 1.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN B 141 GLN D 51 GLN D 221 GLN C 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120411 restraints weight = 11817.096| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.90 r_work: 0.3204 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13080 Z= 0.175 Angle : 0.589 6.822 17960 Z= 0.290 Chirality : 0.041 0.217 2255 Planarity : 0.004 0.041 2150 Dihedral : 6.213 70.692 2275 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.42 % Allowed : 16.53 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.22), residues: 1535 helix: 3.17 (0.20), residues: 480 sheet: 0.58 (0.26), residues: 425 loop : -0.12 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 88 TYR 0.023 0.002 TYR A 176 PHE 0.017 0.002 PHE E 385 TRP 0.012 0.001 TRP C 389 HIS 0.004 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00401 (13040) covalent geometry : angle 0.57749 (17850) SS BOND : bond 0.00231 ( 10) SS BOND : angle 0.97378 ( 20) hydrogen bonds : bond 0.04613 ( 669) hydrogen bonds : angle 4.26170 ( 2202) link_BETA1-4 : bond 0.00439 ( 20) link_BETA1-4 : angle 1.80878 ( 60) link_NAG-ASN : bond 0.00183 ( 10) link_NAG-ASN : angle 1.41379 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 246 time to evaluate : 0.455 Fit side-chains REVERT: A 47 GLN cc_start: 0.5264 (tt0) cc_final: 0.5009 (tp40) REVERT: A 146 LYS cc_start: 0.8390 (mttm) cc_final: 0.7774 (mttp) REVERT: A 208 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8079 (mttp) REVERT: A 210 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7613 (pt0) REVERT: B 49 SER cc_start: 0.7747 (m) cc_final: 0.7378 (p) REVERT: B 85 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8134 (mt) REVERT: B 208 LYS cc_start: 0.7978 (mtmt) cc_final: 0.7315 (mttp) REVERT: B 257 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7285 (ptt180) REVERT: B 368 ARG cc_start: 0.7067 (mtm110) cc_final: 0.6588 (mtm-85) REVERT: B 372 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8034 (mm) REVERT: D 86 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8571 (tt) REVERT: D 88 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7278 (ttt90) REVERT: D 167 ASP cc_start: 0.8601 (p0) cc_final: 0.8145 (p0) REVERT: C 54 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7333 (t0) REVERT: C 78 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7044 (mtm110) REVERT: C 113 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: C 154 GLU cc_start: 0.9050 (tt0) cc_final: 0.8556 (tt0) REVERT: C 160 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: C 369 ILE cc_start: 0.8604 (mt) cc_final: 0.8194 (mm) outliers start: 75 outliers final: 54 residues processed: 286 average time/residue: 0.5730 time to fit residues: 178.4372 Evaluate side-chains 301 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 237 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 55 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 210 GLN B 141 GLN D 73 ASN D 221 GLN C 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.147274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120649 restraints weight = 11949.956| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.86 r_work: 0.3238 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13080 Z= 0.127 Angle : 0.549 6.361 17960 Z= 0.271 Chirality : 0.040 0.212 2255 Planarity : 0.004 0.042 2150 Dihedral : 5.913 64.427 2275 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.05 % Allowed : 17.40 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.22), residues: 1535 helix: 3.28 (0.21), residues: 480 sheet: 0.54 (0.26), residues: 415 loop : -0.04 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 88 TYR 0.024 0.002 TYR A 176 PHE 0.017 0.002 PHE E 385 TRP 0.011 0.001 TRP C 389 HIS 0.003 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00276 (13040) covalent geometry : angle 0.53719 (17850) SS BOND : bond 0.00150 ( 10) SS BOND : angle 0.71647 ( 20) hydrogen bonds : bond 0.04358 ( 669) hydrogen bonds : angle 4.14504 ( 2202) link_BETA1-4 : bond 0.00429 ( 20) link_BETA1-4 : angle 1.76103 ( 60) link_NAG-ASN : bond 0.00095 ( 10) link_NAG-ASN : angle 1.58071 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 244 time to evaluate : 0.489 Fit side-chains REVERT: A 47 GLN cc_start: 0.5309 (tt0) cc_final: 0.5051 (tp40) REVERT: A 146 LYS cc_start: 0.8373 (mttm) cc_final: 0.7763 (mttp) REVERT: A 208 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8021 (mttp) REVERT: A 210 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7554 (pt0) REVERT: B 49 SER cc_start: 0.7846 (m) cc_final: 0.7482 (p) REVERT: B 85 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8087 (mp) REVERT: B 208 LYS cc_start: 0.8010 (mtmt) cc_final: 0.7308 (mttp) REVERT: B 257 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7347 (ptt180) REVERT: B 368 ARG cc_start: 0.7049 (mtm110) cc_final: 0.6583 (mtm-85) REVERT: B 372 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8033 (mm) REVERT: D 86 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8589 (tt) REVERT: D 88 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7274 (ttt90) REVERT: D 167 ASP cc_start: 0.8501 (p0) cc_final: 0.8012 (p0) REVERT: C 54 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7326 (t0) REVERT: C 78 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.6913 (mtm110) REVERT: C 113 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: C 154 GLU cc_start: 0.9032 (tt0) cc_final: 0.8524 (tt0) REVERT: C 160 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: C 369 ILE cc_start: 0.8590 (mt) cc_final: 0.8185 (mm) outliers start: 70 outliers final: 49 residues processed: 281 average time/residue: 0.5682 time to fit residues: 173.3241 Evaluate side-chains 297 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 238 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 111 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 210 GLN B 141 GLN D 221 GLN C 210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.116407 restraints weight = 12046.718| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.87 r_work: 0.3167 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13080 Z= 0.239 Angle : 0.657 7.439 17960 Z= 0.324 Chirality : 0.043 0.249 2255 Planarity : 0.004 0.042 2150 Dihedral : 6.179 61.337 2275 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.98 % Allowed : 17.47 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.21), residues: 1535 helix: 2.95 (0.21), residues: 480 sheet: 0.45 (0.26), residues: 425 loop : -0.18 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 88 TYR 0.032 0.002 TYR A 176 PHE 0.020 0.002 PHE E 385 TRP 0.013 0.002 TRP E 389 HIS 0.007 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00561 (13040) covalent geometry : angle 0.64564 (17850) SS BOND : bond 0.00321 ( 10) SS BOND : angle 1.31161 ( 20) hydrogen bonds : bond 0.04958 ( 669) hydrogen bonds : angle 4.41392 ( 2202) link_BETA1-4 : bond 0.00419 ( 20) link_BETA1-4 : angle 1.84568 ( 60) link_NAG-ASN : bond 0.00355 ( 10) link_NAG-ASN : angle 1.61321 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 243 time to evaluate : 0.478 Fit side-chains REVERT: A 47 GLN cc_start: 0.5260 (tt0) cc_final: 0.5004 (tp40) REVERT: A 146 LYS cc_start: 0.8388 (mttm) cc_final: 0.7749 (mttp) REVERT: A 167 ASP cc_start: 0.8594 (p0) cc_final: 0.8345 (p0) REVERT: A 208 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8077 (mttp) REVERT: A 210 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7638 (pt0) REVERT: B 85 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8176 (mp) REVERT: B 208 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7693 (mtmm) REVERT: B 257 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7286 (ptt180) REVERT: B 302 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8247 (mt) REVERT: B 368 ARG cc_start: 0.7102 (mtm110) cc_final: 0.6889 (mtm-85) REVERT: D 86 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8574 (tt) REVERT: D 88 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7326 (ttt90) REVERT: D 167 ASP cc_start: 0.8712 (p0) cc_final: 0.8311 (p0) REVERT: C 54 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7320 (t0) REVERT: C 78 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7046 (mtm110) REVERT: C 113 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: C 154 GLU cc_start: 0.9120 (tt0) cc_final: 0.8660 (tt0) REVERT: C 160 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: C 369 ILE cc_start: 0.8623 (mt) cc_final: 0.8209 (mm) outliers start: 69 outliers final: 50 residues processed: 280 average time/residue: 0.5617 time to fit residues: 171.4705 Evaluate side-chains 294 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 234 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 210 GLN B 141 GLN D 188 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS C 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.148700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.121414 restraints weight = 12046.300| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.90 r_work: 0.3238 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13080 Z= 0.119 Angle : 0.544 6.277 17960 Z= 0.270 Chirality : 0.039 0.212 2255 Planarity : 0.004 0.042 2150 Dihedral : 5.679 57.330 2275 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.26 % Allowed : 18.56 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.22), residues: 1535 helix: 3.21 (0.21), residues: 480 sheet: 0.48 (0.26), residues: 415 loop : -0.08 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 88 TYR 0.028 0.002 TYR A 176 PHE 0.020 0.002 PHE E 385 TRP 0.012 0.001 TRP C 389 HIS 0.002 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00255 (13040) covalent geometry : angle 0.53344 (17850) SS BOND : bond 0.00162 ( 10) SS BOND : angle 0.62071 ( 20) hydrogen bonds : bond 0.04325 ( 669) hydrogen bonds : angle 4.14639 ( 2202) link_BETA1-4 : bond 0.00421 ( 20) link_BETA1-4 : angle 1.71596 ( 60) link_NAG-ASN : bond 0.00117 ( 10) link_NAG-ASN : angle 1.39850 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 234 time to evaluate : 0.392 Fit side-chains REVERT: A 47 GLN cc_start: 0.5238 (tt0) cc_final: 0.4984 (tp40) REVERT: A 146 LYS cc_start: 0.8364 (mttm) cc_final: 0.7769 (mttp) REVERT: A 208 LYS cc_start: 0.8571 (mtmt) cc_final: 0.7953 (mttp) REVERT: A 210 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7426 (pt0) REVERT: A 364 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: B 49 SER cc_start: 0.7787 (m) cc_final: 0.7423 (p) REVERT: B 85 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8069 (mp) REVERT: B 201 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7493 (tp30) REVERT: B 208 LYS cc_start: 0.8079 (mtmt) cc_final: 0.7730 (mtmm) REVERT: B 257 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7327 (ptt180) REVERT: B 302 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8257 (mt) REVERT: B 368 ARG cc_start: 0.7053 (mtm110) cc_final: 0.6793 (mtm-85) REVERT: D 85 LEU cc_start: 0.8986 (mp) cc_final: 0.8733 (mt) REVERT: D 88 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7294 (ttt90) REVERT: D 167 ASP cc_start: 0.8516 (p0) cc_final: 0.8025 (p0) REVERT: C 54 ASN cc_start: 0.7683 (OUTLIER) cc_final: 0.7333 (t0) REVERT: C 78 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.6970 (mtm110) REVERT: C 113 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: C 146 LYS cc_start: 0.8685 (mtmt) cc_final: 0.8440 (mptt) REVERT: C 154 GLU cc_start: 0.9076 (tt0) cc_final: 0.8594 (tt0) REVERT: C 160 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: C 369 ILE cc_start: 0.8589 (mt) cc_final: 0.8185 (mm) outliers start: 59 outliers final: 44 residues processed: 265 average time/residue: 0.6059 time to fit residues: 174.1351 Evaluate side-chains 281 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 90 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 GLN D 188 GLN D 221 GLN D 382 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.146105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119442 restraints weight = 12076.242| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.86 r_work: 0.3223 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.212 13080 Z= 0.220 Angle : 0.859 59.198 17960 Z= 0.477 Chirality : 0.042 0.517 2255 Planarity : 0.005 0.141 2150 Dihedral : 5.682 57.341 2275 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.04 % Allowed : 18.84 % Favored : 77.11 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.21), residues: 1535 helix: 3.20 (0.21), residues: 480 sheet: 0.47 (0.26), residues: 415 loop : -0.08 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 78 TYR 0.021 0.002 TYR A 176 PHE 0.018 0.002 PHE E 385 TRP 0.012 0.001 TRP C 389 HIS 0.003 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00456 (13040) covalent geometry : angle 0.85312 (17850) SS BOND : bond 0.00284 ( 10) SS BOND : angle 0.71828 ( 20) hydrogen bonds : bond 0.04414 ( 669) hydrogen bonds : angle 4.16874 ( 2202) link_BETA1-4 : bond 0.00418 ( 20) link_BETA1-4 : angle 1.72547 ( 60) link_NAG-ASN : bond 0.00129 ( 10) link_NAG-ASN : angle 1.38702 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5161.07 seconds wall clock time: 88 minutes 31.19 seconds (5311.19 seconds total)