Starting phenix.real_space_refine on Sun May 3 11:58:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9leu_63034/05_2026/9leu_63034.cif Found real_map, /net/cci-nas-00/data/ceres_data/9leu_63034/05_2026/9leu_63034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9leu_63034/05_2026/9leu_63034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9leu_63034/05_2026/9leu_63034.map" model { file = "/net/cci-nas-00/data/ceres_data/9leu_63034/05_2026/9leu_63034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9leu_63034/05_2026/9leu_63034.cif" } resolution = 2.63 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= 0.157 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 8280 2.51 5 N 2070 2.21 5 O 2325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s 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: 12735 Number of models: 1 Model: "" Number of chains: 20 Chain: "C" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2468 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2468 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2468 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2468 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2468 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: "E" 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: 3.46, per 1000 atoms: 0.27 Number of scatterers: 12735 At special positions: 0 Unit cell: (99.724, 97.86, 123.956, 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 2325 8.00 N 2070 7.00 C 8280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 289 " - pdb=" SG CYS D 394 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 394 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG 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 C 55 " " NAG G 1 " - " ASN C 170 " " NAG H 1 " - " ASN A 55 " " NAG I 1 " - " ASN A 170 " " NAG J 1 " - " ASN B 55 " " NAG K 1 " - " ASN B 170 " " NAG L 1 " - " ASN D 55 " " NAG M 1 " - " ASN D 170 " " NAG N 1 " - " ASN E 55 " " NAG O 1 " - " ASN E 170 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 582.0 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 36.0% alpha, 38.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 231 through 252 removed outlier: 4.657A 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: 4.042A pdb=" N TYR C 295 " --> pdb=" O PRO C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 391 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: 4.284A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 322 removed outlier: 4.042A 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 282 removed outlier: 4.285A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 322 removed outlier: 4.042A 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 '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 '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 sheet with id=AA1, first strand: chain 'C' and resid 107 through 111 removed outlier: 6.211A 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: 4.623A 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: 6.603A pdb=" N THR C 152 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL C 128 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU C 154 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 107 through 111 removed outlier: 6.211A 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: 4.623A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 6.852A 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: 7.079A pdb=" N ARG C 88 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 5.774A 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: 5.355A 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: 8.059A 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=AA3, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AA4, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AA5, 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: 5.117A 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: 4.863A pdb=" N TRP A 130 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR A 152 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL A 128 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU A 154 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing sheet with id=AA6, 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: 5.117A 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: 4.650A 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: 5.290A pdb=" N VAL A 68 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ARG A 88 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL A 66 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N SER A 90 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 5.356A 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: 8.059A 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=AA7, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA8, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 111 removed outlier: 6.211A 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: 4.624A 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: 4.864A pdb=" N TRP B 130 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR B 152 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.674A 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=AB1, first strand: chain 'B' and resid 107 through 111 removed outlier: 6.211A 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: 4.624A 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: 4.650A pdb=" N VAL B 74 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 6.957A 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: 7.080A pdb=" N ARG B 88 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL B 66 " --> pdb=" O ARG B 88 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N SER B 90 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 5.355A 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: 8.058A 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=AB2, first strand: chain 'B' and resid 121 through 122 Processing sheet with id=AB3, first strand: chain 'B' 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: 5.118A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.622A 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: 4.864A pdb=" N TRP D 130 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR D 152 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL D 128 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 6.811A 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: 5.118A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR D 80 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.650A 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: 5.290A 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: 7.208A pdb=" N SER D 90 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 5.355A 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: 8.058A 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 '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: 5.118A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.623A 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: 6.602A pdb=" N THR E 152 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL E 128 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU E 154 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AB9, 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: 5.118A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.623A 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: 4.651A pdb=" N VAL E 74 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU E 86 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL E 68 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ARG E 88 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL E 66 " --> pdb=" O ARG E 88 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N SER E 90 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL E 64 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 8.737A 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=AC1, first strand: chain 'E' and resid 121 through 122 Processing sheet with id=AC2, first strand: chain 'E' and resid 121 through 122 755 hydrogen bonds defined for protein. 2205 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: 2.40 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3925 1.34 - 1.46: 3023 1.46 - 1.58: 6007 1.58 - 1.70: 0 1.70 - 1.81: 75 Bond restraints: 13030 Sorted by residual: bond pdb=" C1 BMA L 3 " pdb=" C2 BMA L 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 ... (remaining 13025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 16789 1.26 - 2.53: 805 2.53 - 3.79: 146 3.79 - 5.05: 69 5.05 - 6.31: 26 Bond angle restraints: 17835 Sorted by residual: angle pdb=" N ARG D 78 " pdb=" CA ARG D 78 " pdb=" C ARG D 78 " ideal model delta sigma weight residual 113.28 109.38 3.90 1.22e+00 6.72e-01 1.02e+01 angle pdb=" N ARG A 78 " pdb=" CA ARG A 78 " pdb=" C ARG A 78 " ideal model delta sigma weight residual 113.28 109.39 3.89 1.22e+00 6.72e-01 1.02e+01 angle pdb=" N ARG C 78 " pdb=" CA ARG C 78 " pdb=" C ARG C 78 " ideal model delta sigma weight residual 113.28 109.42 3.86 1.22e+00 6.72e-01 1.00e+01 angle pdb=" N ARG B 78 " pdb=" CA ARG B 78 " pdb=" C ARG B 78 " ideal model delta sigma weight residual 113.28 109.44 3.84 1.22e+00 6.72e-01 9.92e+00 angle pdb=" N ARG E 78 " pdb=" CA ARG E 78 " pdb=" C ARG E 78 " ideal model delta sigma weight residual 113.28 109.45 3.83 1.22e+00 6.72e-01 9.83e+00 ... (remaining 17830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.06: 7610 22.06 - 44.12: 340 44.12 - 66.18: 50 66.18 - 88.23: 80 88.23 - 110.29: 40 Dihedral angle restraints: 8120 sinusoidal: 3510 harmonic: 4610 Sorted by residual: dihedral pdb=" O4 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.42 110.29 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" O4 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C5 BMA J 3 " pdb=" O5 BMA J 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.43 110.28 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.44 110.27 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 8117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1871 0.057 - 0.113: 316 0.113 - 0.170: 52 0.170 - 0.226: 1 0.226 - 0.283: 10 Chirality restraints: 2250 Sorted by residual: chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 2247 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 234 " -0.005 2.00e-02 2.50e+03 1.08e-02 1.16e+00 pdb=" C ILE A 234 " 0.019 2.00e-02 2.50e+03 pdb=" O ILE A 234 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE A 235 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 234 " -0.005 2.00e-02 2.50e+03 1.07e-02 1.15e+00 pdb=" C ILE B 234 " 0.019 2.00e-02 2.50e+03 pdb=" O ILE B 234 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE B 235 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 234 " 0.005 2.00e-02 2.50e+03 1.07e-02 1.15e+00 pdb=" C ILE C 234 " -0.019 2.00e-02 2.50e+03 pdb=" O ILE C 234 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE C 235 " 0.006 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1348 2.75 - 3.29: 12043 3.29 - 3.82: 21903 3.82 - 4.36: 25759 4.36 - 4.90: 44790 Nonbonded interactions: 105843 Sorted by model distance: nonbonded pdb=" OD2 ASP B 142 " pdb=" ND1 HIS B 144 " model vdw 2.212 3.120 nonbonded pdb=" OD2 ASP E 142 " pdb=" ND1 HIS E 144 " model vdw 2.212 3.120 nonbonded pdb=" OD2 ASP A 142 " pdb=" ND1 HIS A 144 " model vdw 2.212 3.120 nonbonded pdb=" OD2 ASP C 142 " pdb=" ND1 HIS C 144 " model vdw 2.213 3.120 nonbonded pdb=" OD2 ASP D 142 " pdb=" ND1 HIS D 144 " model vdw 2.213 3.120 ... (remaining 105838 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' 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: 1.820 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.820 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 : 0.004 0.031 13070 Z= 0.194 Angle : 0.698 6.313 17945 Z= 0.354 Chirality : 0.047 0.283 2250 Planarity : 0.004 0.025 2150 Dihedral : 17.868 110.293 5070 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 1.97 (0.22), residues: 1535 helix: 2.52 (0.21), residues: 495 sheet: 1.71 (0.26), residues: 420 loop : 0.03 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 78 TYR 0.012 0.001 TYR E 272 PHE 0.010 0.002 PHE D 220 TRP 0.013 0.001 TRP A 112 HIS 0.004 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00402 (13030) covalent geometry : angle 0.69056 (17835) SS BOND : bond 0.00141 ( 10) SS BOND : angle 0.83487 ( 20) hydrogen bonds : bond 0.13273 ( 670) hydrogen bonds : angle 6.45671 ( 2205) link_BETA1-4 : bond 0.00542 ( 20) link_BETA1-4 : angle 1.57489 ( 60) link_NAG-ASN : bond 0.00071 ( 10) link_NAG-ASN : angle 1.61560 ( 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 270 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.445 Fit side-chains REVERT: C 106 HIS cc_start: 0.7042 (m-70) cc_final: 0.6821 (m90) REVERT: C 215 GLN cc_start: 0.6808 (mt0) cc_final: 0.6586 (mt0) REVERT: A 221 GLN cc_start: 0.8584 (tt0) cc_final: 0.8254 (tt0) REVERT: E 129 ASP cc_start: 0.8039 (t0) cc_final: 0.7777 (t70) REVERT: E 227 LYS cc_start: 0.8828 (pttt) cc_final: 0.8581 (pttp) outliers start: 0 outliers final: 2 residues processed: 270 average time/residue: 0.6846 time to fit residues: 198.7709 Evaluate side-chains 219 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 50 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.0020 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 GLN C 221 GLN C 382 GLN A 215 GLN A 382 GLN B 215 GLN B 221 GLN B 382 GLN D 54 ASN D 215 GLN D 221 GLN D 382 GLN E 180 ASN E 215 GLN E 221 GLN E 382 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.143139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.116152 restraints weight = 11655.989| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.69 r_work: 0.3166 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13070 Z= 0.193 Angle : 0.668 5.692 17945 Z= 0.320 Chirality : 0.045 0.152 2250 Planarity : 0.004 0.030 2150 Dihedral : 12.189 62.204 2279 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.32 % Allowed : 8.84 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.21), residues: 1535 helix: 2.52 (0.21), residues: 495 sheet: 1.50 (0.25), residues: 420 loop : -0.16 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 320 TYR 0.012 0.002 TYR E 272 PHE 0.014 0.002 PHE D 220 TRP 0.010 0.002 TRP A 389 HIS 0.005 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00458 (13030) covalent geometry : angle 0.64872 (17835) SS BOND : bond 0.00210 ( 10) SS BOND : angle 1.37504 ( 20) hydrogen bonds : bond 0.04953 ( 670) hydrogen bonds : angle 4.88347 ( 2205) link_BETA1-4 : bond 0.00538 ( 20) link_BETA1-4 : angle 2.55449 ( 60) link_NAG-ASN : bond 0.00134 ( 10) link_NAG-ASN : angle 1.54375 ( 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 260 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 0.500 Fit side-chains REVERT: C 129 ASP cc_start: 0.8516 (t0) cc_final: 0.8272 (t70) REVERT: C 186 GLU cc_start: 0.8578 (tt0) cc_final: 0.8292 (tt0) REVERT: A 221 GLN cc_start: 0.8779 (tt0) cc_final: 0.8355 (tt0) REVERT: A 227 LYS cc_start: 0.8925 (pttt) cc_final: 0.8560 (pttp) REVERT: B 65 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7810 (mtt-85) REVERT: B 148 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8032 (p0) REVERT: D 188 GLN cc_start: 0.8306 (tt0) cc_final: 0.8096 (tt0) REVERT: D 201 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7375 (tt0) REVERT: D 227 LYS cc_start: 0.8891 (pttt) cc_final: 0.8547 (pttp) REVERT: E 129 ASP cc_start: 0.8644 (t0) cc_final: 0.8336 (t70) REVERT: E 227 LYS cc_start: 0.8852 (pttt) cc_final: 0.8550 (pttp) outliers start: 32 outliers final: 22 residues processed: 241 average time/residue: 0.5916 time to fit residues: 154.8345 Evaluate side-chains 244 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain A residue 148 ASN 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 B residue 65 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 GLN C 221 GLN A 215 GLN B 215 GLN B 221 GLN D 54 ASN D 215 GLN D 221 GLN D 281 GLN E 215 GLN E 221 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119980 restraints weight = 11612.553| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.85 r_work: 0.3187 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13070 Z= 0.160 Angle : 0.575 5.236 17945 Z= 0.282 Chirality : 0.042 0.151 2250 Planarity : 0.004 0.027 2150 Dihedral : 7.171 51.547 2279 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.61 % Allowed : 11.74 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.21), residues: 1535 helix: 2.63 (0.21), residues: 495 sheet: 1.26 (0.27), residues: 370 loop : -0.10 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 320 TYR 0.013 0.002 TYR E 272 PHE 0.013 0.002 PHE B 220 TRP 0.010 0.001 TRP A 116 HIS 0.004 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00369 (13030) covalent geometry : angle 0.55905 (17835) SS BOND : bond 0.00129 ( 10) SS BOND : angle 0.83056 ( 20) hydrogen bonds : bond 0.04588 ( 670) hydrogen bonds : angle 4.60118 ( 2205) link_BETA1-4 : bond 0.00522 ( 20) link_BETA1-4 : angle 2.16780 ( 60) link_NAG-ASN : bond 0.00156 ( 10) link_NAG-ASN : angle 1.51372 ( 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 261 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 0.482 Fit side-chains REVERT: C 186 GLU cc_start: 0.8651 (tt0) cc_final: 0.8398 (tt0) REVERT: A 160 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: A 188 GLN cc_start: 0.8559 (tt0) cc_final: 0.8275 (tt0) REVERT: A 227 LYS cc_start: 0.8954 (pttt) cc_final: 0.8656 (pttp) REVERT: B 65 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8052 (mtt-85) REVERT: B 154 GLU cc_start: 0.9170 (tt0) cc_final: 0.8921 (tt0) REVERT: B 227 LYS cc_start: 0.8939 (pttt) cc_final: 0.8648 (pttp) REVERT: D 201 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: D 227 LYS cc_start: 0.8922 (pttt) cc_final: 0.8622 (pttp) REVERT: E 160 GLU cc_start: 0.8373 (tt0) cc_final: 0.7960 (tm-30) REVERT: E 201 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: E 227 LYS cc_start: 0.8894 (pttt) cc_final: 0.8601 (pttp) outliers start: 36 outliers final: 21 residues processed: 237 average time/residue: 0.6356 time to fit residues: 162.7990 Evaluate side-chains 243 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain A residue 160 GLU 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 B residue 65 ARG Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 285 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 58 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 146 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 GLN C 221 GLN A 215 GLN A 221 GLN B 215 GLN B 221 GLN D 54 ASN D 215 GLN D 221 GLN D 281 GLN E 148 ASN E 215 GLN E 221 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.115604 restraints weight = 11778.586| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.86 r_work: 0.3147 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13070 Z= 0.225 Angle : 0.631 5.792 17945 Z= 0.311 Chirality : 0.043 0.139 2250 Planarity : 0.004 0.026 2150 Dihedral : 6.772 55.833 2275 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.70 % Allowed : 14.35 % Favored : 81.96 % 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: 1.39 (0.21), residues: 1535 helix: 2.47 (0.21), residues: 490 sheet: 0.81 (0.26), residues: 415 loop : -0.21 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 78 TYR 0.014 0.002 TYR B 176 PHE 0.019 0.002 PHE D 220 TRP 0.011 0.002 TRP C 389 HIS 0.006 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00539 (13030) covalent geometry : angle 0.61806 (17835) SS BOND : bond 0.00315 ( 10) SS BOND : angle 1.25033 ( 20) hydrogen bonds : bond 0.04872 ( 670) hydrogen bonds : angle 4.72390 ( 2205) link_BETA1-4 : bond 0.00428 ( 20) link_BETA1-4 : angle 1.88383 ( 60) link_NAG-ASN : bond 0.00215 ( 10) link_NAG-ASN : angle 1.63829 ( 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 265 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 0.524 Fit side-chains REVERT: C 186 GLU cc_start: 0.8641 (tt0) cc_final: 0.8383 (tt0) REVERT: A 160 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7214 (tm-30) REVERT: A 188 GLN cc_start: 0.8589 (tt0) cc_final: 0.8325 (tt0) REVERT: A 227 LYS cc_start: 0.8946 (pttt) cc_final: 0.8638 (pttp) REVERT: A 368 ARG cc_start: 0.7776 (mtm180) cc_final: 0.7479 (mmm-85) REVERT: B 65 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8139 (mtt-85) REVERT: B 142 ASP cc_start: 0.7657 (p0) cc_final: 0.7390 (p0) REVERT: B 160 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7938 (tp30) REVERT: D 227 LYS cc_start: 0.8930 (pttt) cc_final: 0.8629 (pttp) REVERT: E 129 ASP cc_start: 0.8694 (t0) cc_final: 0.8394 (t70) REVERT: E 227 LYS cc_start: 0.8930 (pttt) cc_final: 0.8663 (pttp) outliers start: 51 outliers final: 29 residues processed: 242 average time/residue: 0.6169 time to fit residues: 161.8392 Evaluate side-chains 240 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 160 GLU 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 211 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 285 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 GLN C 221 GLN A 215 GLN A 221 GLN B 215 GLN B 221 GLN D 54 ASN D 215 GLN D 281 GLN E 215 GLN E 221 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.148291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120555 restraints weight = 11770.093| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.85 r_work: 0.3185 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13070 Z= 0.128 Angle : 0.527 5.167 17945 Z= 0.263 Chirality : 0.039 0.126 2250 Planarity : 0.004 0.023 2150 Dihedral : 6.450 59.766 2275 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.90 % Allowed : 16.52 % Favored : 80.58 % 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: 1.63 (0.22), residues: 1535 helix: 2.71 (0.21), residues: 495 sheet: 1.14 (0.27), residues: 370 loop : -0.20 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 320 TYR 0.017 0.002 TYR E 176 PHE 0.015 0.001 PHE D 220 TRP 0.009 0.001 TRP C 389 HIS 0.003 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00289 (13030) covalent geometry : angle 0.51680 (17835) SS BOND : bond 0.00076 ( 10) SS BOND : angle 0.62627 ( 20) hydrogen bonds : bond 0.04273 ( 670) hydrogen bonds : angle 4.42161 ( 2205) link_BETA1-4 : bond 0.00461 ( 20) link_BETA1-4 : angle 1.61574 ( 60) link_NAG-ASN : bond 0.00162 ( 10) link_NAG-ASN : angle 1.45235 ( 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 265 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 0.578 Fit side-chains REVERT: C 148 ASN cc_start: 0.9085 (m-40) cc_final: 0.8779 (m-40) REVERT: C 186 GLU cc_start: 0.8636 (tt0) cc_final: 0.8381 (tt0) REVERT: A 86 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8861 (tt) REVERT: A 160 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8089 (tp30) REVERT: A 188 GLN cc_start: 0.8565 (tt0) cc_final: 0.8297 (tt0) REVERT: A 227 LYS cc_start: 0.8936 (pttt) cc_final: 0.8642 (pttp) REVERT: A 368 ARG cc_start: 0.7776 (mtm180) cc_final: 0.7484 (mmm-85) REVERT: B 65 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8069 (mtt-85) REVERT: B 142 ASP cc_start: 0.7667 (p0) cc_final: 0.7396 (p0) REVERT: B 154 GLU cc_start: 0.9139 (tt0) cc_final: 0.8901 (tt0) REVERT: B 160 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: B 227 LYS cc_start: 0.8871 (pttt) cc_final: 0.8573 (pttp) REVERT: D 201 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: D 227 LYS cc_start: 0.8898 (pttt) cc_final: 0.8609 (pttp) REVERT: E 160 GLU cc_start: 0.8356 (tt0) cc_final: 0.7964 (tm-30) REVERT: E 227 LYS cc_start: 0.8887 (pttt) cc_final: 0.8603 (pttp) outliers start: 40 outliers final: 26 residues processed: 240 average time/residue: 0.5968 time to fit residues: 155.4155 Evaluate side-chains 246 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 160 GLU 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 211 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 50 ILE 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 285 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 35 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 GLN C 221 GLN A 215 GLN B 215 GLN B 221 GLN D 54 ASN D 215 GLN D 281 GLN E 215 GLN E 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.141974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113699 restraints weight = 11787.631| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.87 r_work: 0.3127 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13070 Z= 0.253 Angle : 0.642 6.110 17945 Z= 0.318 Chirality : 0.044 0.145 2250 Planarity : 0.004 0.034 2150 Dihedral : 6.206 56.387 2275 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.19 % Allowed : 16.67 % Favored : 80.14 % 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: 1.26 (0.21), residues: 1535 helix: 2.42 (0.21), residues: 490 sheet: 0.63 (0.26), residues: 425 loop : -0.27 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 320 TYR 0.015 0.002 TYR D 205 PHE 0.015 0.002 PHE D 220 TRP 0.011 0.002 TRP C 389 HIS 0.006 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00608 (13030) covalent geometry : angle 0.63191 (17835) SS BOND : bond 0.00391 ( 10) SS BOND : angle 1.34016 ( 20) hydrogen bonds : bond 0.04937 ( 670) hydrogen bonds : angle 4.69815 ( 2205) link_BETA1-4 : bond 0.00403 ( 20) link_BETA1-4 : angle 1.68052 ( 60) link_NAG-ASN : bond 0.00227 ( 10) link_NAG-ASN : angle 1.60484 ( 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 263 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.524 Fit side-chains REVERT: C 81 MET cc_start: 0.9225 (ptt) cc_final: 0.8953 (ptt) REVERT: C 186 GLU cc_start: 0.8665 (tt0) cc_final: 0.8414 (tt0) REVERT: A 86 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8855 (tt) REVERT: A 160 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: A 188 GLN cc_start: 0.8623 (tt0) cc_final: 0.8287 (tt0) REVERT: A 227 LYS cc_start: 0.8957 (pttt) cc_final: 0.8672 (pttp) REVERT: A 368 ARG cc_start: 0.7824 (mtm180) cc_final: 0.7528 (mmm-85) REVERT: B 65 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8178 (mtt-85) REVERT: B 142 ASP cc_start: 0.7672 (p0) cc_final: 0.7442 (p0) REVERT: D 142 ASP cc_start: 0.7635 (p0) cc_final: 0.7328 (p0) REVERT: D 227 LYS cc_start: 0.8925 (pttt) cc_final: 0.8634 (pttp) REVERT: E 129 ASP cc_start: 0.8681 (t0) cc_final: 0.8431 (t70) REVERT: E 160 GLU cc_start: 0.8400 (tt0) cc_final: 0.7988 (tm-30) REVERT: E 227 LYS cc_start: 0.8911 (pttt) cc_final: 0.8640 (pttp) outliers start: 44 outliers final: 29 residues processed: 246 average time/residue: 0.5638 time to fit residues: 151.2298 Evaluate side-chains 245 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 160 GLU 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 211 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 285 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 46 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 158 ASN C 215 GLN C 221 GLN A 215 GLN B 215 GLN B 221 GLN D 54 ASN D 215 GLN D 281 GLN E 215 GLN E 221 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.147763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119979 restraints weight = 11700.823| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.85 r_work: 0.3198 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13070 Z= 0.149 Angle : 0.548 5.473 17945 Z= 0.274 Chirality : 0.040 0.129 2250 Planarity : 0.004 0.034 2150 Dihedral : 5.460 46.539 2275 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.41 % Allowed : 16.67 % Favored : 79.93 % 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: 1.44 (0.22), residues: 1535 helix: 2.66 (0.21), residues: 490 sheet: 0.96 (0.27), residues: 370 loop : -0.32 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 320 TYR 0.015 0.002 TYR E 176 PHE 0.014 0.002 PHE D 220 TRP 0.010 0.001 TRP A 116 HIS 0.003 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00345 (13030) covalent geometry : angle 0.53876 (17835) SS BOND : bond 0.00124 ( 10) SS BOND : angle 0.75328 ( 20) hydrogen bonds : bond 0.04393 ( 670) hydrogen bonds : angle 4.46436 ( 2205) link_BETA1-4 : bond 0.00435 ( 20) link_BETA1-4 : angle 1.51942 ( 60) link_NAG-ASN : bond 0.00133 ( 10) link_NAG-ASN : angle 1.47594 ( 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 258 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 0.396 Fit side-chains REVERT: C 186 GLU cc_start: 0.8620 (tt0) cc_final: 0.8366 (tt0) REVERT: A 86 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8860 (tt) REVERT: A 160 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8102 (tp30) REVERT: A 188 GLN cc_start: 0.8594 (tt0) cc_final: 0.8343 (tt0) REVERT: A 227 LYS cc_start: 0.8929 (pttt) cc_final: 0.8634 (pttp) REVERT: A 368 ARG cc_start: 0.7811 (mtm180) cc_final: 0.7523 (mmm-85) REVERT: B 65 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8129 (mtt-85) REVERT: B 86 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8768 (tt) REVERT: B 142 ASP cc_start: 0.7695 (p0) cc_final: 0.7465 (p0) REVERT: B 160 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7944 (tp30) REVERT: D 142 ASP cc_start: 0.7672 (p0) cc_final: 0.7355 (p0) REVERT: D 227 LYS cc_start: 0.8916 (pttt) cc_final: 0.8638 (pttp) REVERT: E 160 GLU cc_start: 0.8376 (tt0) cc_final: 0.7964 (tm-30) REVERT: E 188 GLN cc_start: 0.8634 (tt0) cc_final: 0.8099 (tt0) REVERT: E 227 LYS cc_start: 0.8880 (pttt) cc_final: 0.8619 (pttp) outliers start: 47 outliers final: 30 residues processed: 235 average time/residue: 0.5688 time to fit residues: 145.6019 Evaluate side-chains 242 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 160 GLU 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 211 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 285 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 150 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 63 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 GLN C 221 GLN B 215 GLN B 221 GLN D 54 ASN D 188 GLN D 215 GLN E 215 GLN E 221 GLN E 281 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.121336 restraints weight = 11718.979| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.85 r_work: 0.3197 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13070 Z= 0.121 Angle : 0.514 5.229 17945 Z= 0.257 Chirality : 0.039 0.126 2250 Planarity : 0.003 0.036 2150 Dihedral : 4.555 30.557 2275 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.97 % Allowed : 17.54 % 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: 1.51 (0.22), residues: 1535 helix: 2.85 (0.21), residues: 490 sheet: 0.54 (0.26), residues: 415 loop : -0.13 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 320 TYR 0.017 0.002 TYR E 176 PHE 0.014 0.001 PHE D 220 TRP 0.008 0.001 TRP D 112 HIS 0.003 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00271 (13030) covalent geometry : angle 0.50472 (17835) SS BOND : bond 0.00065 ( 10) SS BOND : angle 0.58214 ( 20) hydrogen bonds : bond 0.04110 ( 670) hydrogen bonds : angle 4.23459 ( 2205) link_BETA1-4 : bond 0.00445 ( 20) link_BETA1-4 : angle 1.44810 ( 60) link_NAG-ASN : bond 0.00123 ( 10) link_NAG-ASN : angle 1.37295 ( 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 259 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.479 Fit side-chains REVERT: C 88 ARG cc_start: 0.8210 (mtt-85) cc_final: 0.7477 (mtm110) REVERT: A 160 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8047 (tp30) REVERT: A 188 GLN cc_start: 0.8573 (tt0) cc_final: 0.8314 (tt0) REVERT: A 227 LYS cc_start: 0.8899 (pttt) cc_final: 0.8617 (pttp) REVERT: A 368 ARG cc_start: 0.7795 (mtm180) cc_final: 0.7511 (mmm-85) REVERT: B 65 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8058 (mtt-85) REVERT: B 86 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8763 (tt) REVERT: B 142 ASP cc_start: 0.7676 (p0) cc_final: 0.7425 (p0) REVERT: B 146 LYS cc_start: 0.8433 (mttm) cc_final: 0.7917 (mttp) REVERT: B 160 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: B 227 LYS cc_start: 0.8847 (pttt) cc_final: 0.8549 (pttp) REVERT: D 227 LYS cc_start: 0.8916 (pttt) cc_final: 0.8640 (pttp) REVERT: E 129 ASP cc_start: 0.8604 (t0) cc_final: 0.8371 (t70) REVERT: E 160 GLU cc_start: 0.8374 (tt0) cc_final: 0.7992 (tm-30) REVERT: E 188 GLN cc_start: 0.8587 (tt0) cc_final: 0.8061 (tt0) REVERT: E 227 LYS cc_start: 0.8837 (pttt) cc_final: 0.8585 (pttp) outliers start: 41 outliers final: 30 residues processed: 239 average time/residue: 0.5353 time to fit residues: 139.8025 Evaluate side-chains 245 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 160 GLU 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 211 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 117 THR 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 E residue 50 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 285 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 80 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 GLN C 221 GLN A 221 GLN B 215 GLN B 221 GLN D 54 ASN D 215 GLN D 221 GLN E 215 GLN E 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.120035 restraints weight = 11850.277| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.86 r_work: 0.3208 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13070 Z= 0.136 Angle : 0.530 5.354 17945 Z= 0.265 Chirality : 0.040 0.128 2250 Planarity : 0.004 0.034 2150 Dihedral : 4.328 21.254 2275 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.90 % Allowed : 17.75 % Favored : 79.35 % 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 (0.22), residues: 1535 helix: 2.83 (0.21), residues: 490 sheet: 0.46 (0.26), residues: 415 loop : -0.10 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 320 TYR 0.026 0.002 TYR E 176 PHE 0.014 0.001 PHE D 220 TRP 0.009 0.001 TRP A 116 HIS 0.003 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00311 (13030) covalent geometry : angle 0.52114 (17835) SS BOND : bond 0.00123 ( 10) SS BOND : angle 0.68408 ( 20) hydrogen bonds : bond 0.04205 ( 670) hydrogen bonds : angle 4.25464 ( 2205) link_BETA1-4 : bond 0.00417 ( 20) link_BETA1-4 : angle 1.44094 ( 60) link_NAG-ASN : bond 0.00106 ( 10) link_NAG-ASN : angle 1.40841 ( 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 249 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 0.344 Fit side-chains REVERT: C 160 GLU cc_start: 0.8324 (tt0) cc_final: 0.7732 (mp0) REVERT: C 186 GLU cc_start: 0.8658 (tt0) cc_final: 0.8394 (tt0) REVERT: A 160 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8065 (tp30) REVERT: A 188 GLN cc_start: 0.8605 (tt0) cc_final: 0.8350 (tt0) REVERT: A 227 LYS cc_start: 0.8918 (pttt) cc_final: 0.8644 (pttp) REVERT: A 368 ARG cc_start: 0.7839 (mtm180) cc_final: 0.7560 (mmm-85) REVERT: B 86 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8796 (tt) REVERT: B 142 ASP cc_start: 0.7692 (p0) cc_final: 0.7468 (p0) REVERT: B 146 LYS cc_start: 0.8457 (mttm) cc_final: 0.7941 (mttp) REVERT: B 160 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7968 (tp30) REVERT: D 227 LYS cc_start: 0.8927 (pttt) cc_final: 0.8657 (pttp) REVERT: E 160 GLU cc_start: 0.8404 (tt0) cc_final: 0.8036 (tm-30) REVERT: E 227 LYS cc_start: 0.8856 (pttt) cc_final: 0.8615 (pttp) outliers start: 40 outliers final: 31 residues processed: 229 average time/residue: 0.5484 time to fit residues: 137.0748 Evaluate side-chains 242 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 160 GLU 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 211 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 117 THR 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 E residue 50 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 117 THR 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 209 THR Chi-restraints excluded: chain E residue 285 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 73 optimal weight: 0.0570 chunk 109 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 GLN C 221 GLN A 221 GLN B 215 GLN B 221 GLN D 54 ASN D 215 GLN E 188 GLN E 215 GLN E 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.150736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.123185 restraints weight = 11763.405| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.86 r_work: 0.3213 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13070 Z= 0.114 Angle : 0.505 5.197 17945 Z= 0.253 Chirality : 0.039 0.125 2250 Planarity : 0.003 0.033 2150 Dihedral : 4.078 15.694 2275 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.54 % Allowed : 18.33 % Favored : 79.13 % 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: 1.52 (0.22), residues: 1535 helix: 2.93 (0.21), residues: 490 sheet: 0.38 (0.26), residues: 415 loop : -0.06 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 320 TYR 0.021 0.002 TYR E 176 PHE 0.013 0.001 PHE D 220 TRP 0.008 0.001 TRP C 389 HIS 0.003 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00253 (13030) covalent geometry : angle 0.49695 (17835) SS BOND : bond 0.00045 ( 10) SS BOND : angle 0.54559 ( 20) hydrogen bonds : bond 0.04032 ( 670) hydrogen bonds : angle 4.12016 ( 2205) link_BETA1-4 : bond 0.00442 ( 20) link_BETA1-4 : angle 1.38450 ( 60) link_NAG-ASN : bond 0.00096 ( 10) link_NAG-ASN : angle 1.35651 ( 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 254 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.557 Fit side-chains REVERT: C 160 GLU cc_start: 0.8289 (tt0) cc_final: 0.7677 (mp0) REVERT: C 186 GLU cc_start: 0.8669 (tt0) cc_final: 0.8409 (tt0) REVERT: A 160 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8003 (tp30) REVERT: A 188 GLN cc_start: 0.8556 (tt0) cc_final: 0.8299 (tt0) REVERT: A 227 LYS cc_start: 0.8883 (pttt) cc_final: 0.8603 (pttp) REVERT: A 368 ARG cc_start: 0.7802 (mtm180) cc_final: 0.7521 (mmm-85) REVERT: B 142 ASP cc_start: 0.7675 (p0) cc_final: 0.7438 (p0) REVERT: B 146 LYS cc_start: 0.8421 (mttm) cc_final: 0.7885 (mttp) REVERT: B 160 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: D 227 LYS cc_start: 0.8911 (pttt) cc_final: 0.8631 (pttp) REVERT: E 63 ASP cc_start: 0.8444 (t70) cc_final: 0.8152 (t70) REVERT: E 160 GLU cc_start: 0.8381 (tt0) cc_final: 0.8026 (tm-30) REVERT: E 188 GLN cc_start: 0.8533 (tt0) cc_final: 0.8155 (tt0) REVERT: E 227 LYS cc_start: 0.8826 (pttt) cc_final: 0.8576 (pttp) outliers start: 35 outliers final: 29 residues processed: 234 average time/residue: 0.5580 time to fit residues: 142.6666 Evaluate side-chains 240 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 160 GLU 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 211 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 117 THR 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 E residue 50 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 285 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 48 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 GLN C 221 GLN B 215 GLN B 221 GLN D 54 ASN D 215 GLN E 215 GLN E 221 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.146281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118402 restraints weight = 11746.888| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.86 r_work: 0.3188 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13070 Z= 0.206 Angle : 0.594 5.924 17945 Z= 0.297 Chirality : 0.042 0.143 2250 Planarity : 0.004 0.033 2150 Dihedral : 4.381 16.051 2275 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.68 % Allowed : 18.55 % Favored : 78.77 % 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: 1.31 (0.22), residues: 1535 helix: 2.63 (0.21), residues: 490 sheet: 0.36 (0.26), residues: 425 loop : -0.15 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 320 TYR 0.030 0.002 TYR E 176 PHE 0.015 0.002 PHE D 220 TRP 0.010 0.002 TRP C 389 HIS 0.005 0.001 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00492 (13030) covalent geometry : angle 0.58542 (17835) SS BOND : bond 0.00292 ( 10) SS BOND : angle 1.05805 ( 20) hydrogen bonds : bond 0.04595 ( 670) hydrogen bonds : angle 4.45199 ( 2205) link_BETA1-4 : bond 0.00390 ( 20) link_BETA1-4 : angle 1.45535 ( 60) link_NAG-ASN : bond 0.00194 ( 10) link_NAG-ASN : angle 1.52612 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4863.33 seconds wall clock time: 83 minutes 31.97 seconds (5011.97 seconds total)