Starting phenix.real_space_refine on Sat Aug 23 03:14:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8blb_16105/08_2025/8blb_16105.cif Found real_map, /net/cci-nas-00/data/ceres_data/8blb_16105/08_2025/8blb_16105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8blb_16105/08_2025/8blb_16105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8blb_16105/08_2025/8blb_16105.map" model { file = "/net/cci-nas-00/data/ceres_data/8blb_16105/08_2025/8blb_16105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8blb_16105/08_2025/8blb_16105.cif" } resolution = 3.3 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= -0.001 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 6115 2.51 5 N 1515 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9400 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "B" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "C" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "D" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "E" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.19, per 1000 atoms: 0.23 Number of scatterers: 9400 At special positions: 0 Unit cell: (96.9, 94.62, 79.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1740 8.00 N 1515 7.00 C 6115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 104 " " NAG B 501 " - " ASN B 104 " " NAG C 501 " - " ASN C 104 " " NAG D 501 " - " ASN D 104 " " NAG E 501 " - " ASN E 104 " " NAG F 1 " - " ASN A 186 " " NAG G 1 " - " ASN A 170 " " NAG H 1 " - " ASN B 186 " " NAG I 1 " - " ASN B 170 " " NAG J 1 " - " ASN C 186 " " NAG K 1 " - " ASN C 170 " " NAG L 1 " - " ASN D 186 " " NAG M 1 " - " ASN D 170 " " NAG N 1 " - " ASN E 186 " " NAG O 1 " - " ASN E 170 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 200.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 15 sheets defined 14.7% alpha, 52.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 32 through 43 Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'B' and resid 32 through 43 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 163 through 166 Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 163 through 166 Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'D' and resid 32 through 43 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 163 through 166 Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'E' and resid 32 through 43 Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 163 through 166 Processing helix chain 'E' and resid 192 through 198 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR A 136 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR A 148 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 154 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR A 136 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR A 148 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN A 72 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR A 83 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE A 70 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TRP A 85 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR A 68 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG A 87 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE A 66 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TYR A 89 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP A 64 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR A 91 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER A 62 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER A 177 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA A 230 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 213 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG A 239 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU A 211 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR B 136 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR B 148 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 154 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR B 136 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR B 148 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN B 72 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR B 83 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE B 70 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N TRP B 85 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR B 68 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ARG B 87 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE B 66 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TYR B 89 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP B 64 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N THR B 91 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N SER B 62 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.871A pdb=" N SER B 177 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA B 230 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 213 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG B 239 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU B 211 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR C 136 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR C 148 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 154 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR C 136 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR C 148 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 72 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR C 83 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE C 70 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TRP C 85 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR C 68 " --> pdb=" O TRP C 85 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ARG C 87 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE C 66 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N TYR C 89 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASP C 64 " --> pdb=" O TYR C 89 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N THR C 91 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER C 62 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER C 177 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA C 230 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C 213 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG C 239 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU C 211 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111 removed outlier: 7.021A pdb=" N TYR D 136 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR D 148 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL D 154 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 111 removed outlier: 7.021A pdb=" N TYR D 136 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR D 148 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN D 72 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR D 83 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE D 70 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TRP D 85 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR D 68 " --> pdb=" O TRP D 85 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG D 87 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE D 66 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TYR D 89 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP D 64 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR D 91 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER D 62 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER D 177 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA D 230 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 213 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG D 239 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU D 211 " --> pdb=" O ARG D 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR E 136 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR E 148 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL E 154 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR E 136 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR E 148 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN E 72 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR E 83 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE E 70 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TRP E 85 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR E 68 " --> pdb=" O TRP E 85 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG E 87 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE E 66 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR E 89 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASP E 64 " --> pdb=" O TYR E 89 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR E 91 " --> pdb=" O SER E 62 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER E 62 " --> pdb=" O THR E 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER E 177 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA E 230 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY E 213 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG E 239 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU E 211 " --> pdb=" O ARG E 239 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1020 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: 1.28 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2855 1.34 - 1.46: 2599 1.46 - 1.58: 4171 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 9675 Sorted by residual: bond pdb=" C12 VTX C 502 " pdb=" N13 VTX C 502 " ideal model delta sigma weight residual 1.404 1.453 -0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C12 VTX D 502 " pdb=" N13 VTX D 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.85e+00 bond pdb=" C12 VTX B 502 " pdb=" N13 VTX B 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" C12 VTX A 502 " pdb=" N13 VTX A 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" C12 VTX E 502 " pdb=" N13 VTX E 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.70e+00 ... (remaining 9670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 12914 1.95 - 3.90: 251 3.90 - 5.86: 20 5.86 - 7.81: 10 7.81 - 9.76: 10 Bond angle restraints: 13205 Sorted by residual: angle pdb=" C15 VTX E 502 " pdb=" C14 VTX E 502 " pdb=" N13 VTX E 502 " ideal model delta sigma weight residual 109.33 119.09 -9.76 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C15 VTX D 502 " pdb=" C14 VTX D 502 " pdb=" N13 VTX D 502 " ideal model delta sigma weight residual 109.33 119.06 -9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C15 VTX A 502 " pdb=" C14 VTX A 502 " pdb=" N13 VTX A 502 " ideal model delta sigma weight residual 109.33 119.05 -9.72 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C15 VTX B 502 " pdb=" C14 VTX B 502 " pdb=" N13 VTX B 502 " ideal model delta sigma weight residual 109.33 119.04 -9.71 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C15 VTX C 502 " pdb=" C14 VTX C 502 " pdb=" N13 VTX C 502 " ideal model delta sigma weight residual 109.33 119.04 -9.71 3.00e+00 1.11e-01 1.05e+01 ... (remaining 13200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.13: 5689 25.13 - 50.25: 316 50.25 - 75.38: 35 75.38 - 100.51: 10 100.51 - 125.63: 5 Dihedral angle restraints: 6055 sinusoidal: 2875 harmonic: 3180 Sorted by residual: dihedral pdb=" C15 VTX A 502 " pdb=" C17 VTX A 502 " pdb=" N16 VTX A 502 " pdb=" C18 VTX A 502 " ideal model delta sinusoidal sigma weight residual -69.32 56.31 -125.63 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C15 VTX C 502 " pdb=" C17 VTX C 502 " pdb=" N16 VTX C 502 " pdb=" C18 VTX C 502 " ideal model delta sinusoidal sigma weight residual -69.32 56.30 -125.62 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C15 VTX D 502 " pdb=" C17 VTX D 502 " pdb=" N16 VTX D 502 " pdb=" C18 VTX D 502 " ideal model delta sinusoidal sigma weight residual -69.32 56.29 -125.61 1 3.00e+01 1.11e-03 1.69e+01 ... (remaining 6052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 892 0.029 - 0.057: 348 0.057 - 0.086: 57 0.086 - 0.115: 135 0.115 - 0.143: 58 Chirality restraints: 1490 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 186 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN E 170 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 186 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 1487 not shown) Planarity restraints: 1635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 98 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO C 99 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 98 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.52e+00 pdb=" N PRO E 99 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 99 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 99 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 98 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO D 99 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " 0.038 5.00e-02 4.00e+02 ... (remaining 1632 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 362 2.72 - 3.26: 8911 3.26 - 3.81: 14685 3.81 - 4.35: 18995 4.35 - 4.90: 33164 Nonbonded interactions: 76117 Sorted by model distance: nonbonded pdb=" OH TYR D 136 " pdb=" O VAL E 117 " model vdw 2.171 3.040 nonbonded pdb=" OH TYR C 136 " pdb=" O VAL D 117 " model vdw 2.233 3.040 nonbonded pdb=" NH2 ARG D 219 " pdb=" OE2 GLU D 231 " model vdw 2.298 3.120 nonbonded pdb=" NH2 ARG A 219 " pdb=" OE2 GLU A 231 " model vdw 2.298 3.120 nonbonded pdb=" NH2 ARG C 219 " pdb=" OE2 GLU C 231 " model vdw 2.298 3.120 ... (remaining 76112 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: 0.02 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.550 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 0.049 9705 Z= 0.208 Angle : 0.663 9.759 13290 Z= 0.291 Chirality : 0.048 0.143 1490 Planarity : 0.005 0.069 1620 Dihedral : 15.177 125.633 3980 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % 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 aren not related in a simple way. whole: -0.87 (0.27), residues: 1045 helix: -0.07 (0.57), residues: 95 sheet: -0.49 (0.25), residues: 395 loop : -0.63 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.007 0.001 TYR E 89 PHE 0.003 0.001 PHE B 125 TRP 0.005 0.001 TRP C 97 HIS 0.001 0.000 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 9675) covalent geometry : angle 0.66116 (13205) SS BOND : bond 0.00153 ( 5) SS BOND : angle 0.12941 ( 10) hydrogen bonds : bond 0.22231 ( 290) hydrogen bonds : angle 9.23933 ( 1020) link_BETA1-4 : bond 0.00280 ( 10) link_BETA1-4 : angle 1.12812 ( 30) link_NAG-ASN : bond 0.00288 ( 15) link_NAG-ASN : angle 0.83541 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.248 Fit side-chains REVERT: A 239 ARG cc_start: 0.6314 (ptm160) cc_final: 0.4596 (ptt180) REVERT: B 140 ARG cc_start: 0.7677 (ttm-80) cc_final: 0.7417 (mtp180) REVERT: B 239 ARG cc_start: 0.6186 (ptm160) cc_final: 0.4666 (ptt180) REVERT: C 103 ASP cc_start: 0.7337 (t70) cc_final: 0.7041 (t0) REVERT: D 103 ASP cc_start: 0.7270 (t70) cc_final: 0.7054 (t0) REVERT: D 212 LEU cc_start: 0.8629 (mt) cc_final: 0.8405 (mt) REVERT: D 239 ARG cc_start: 0.5887 (ptm160) cc_final: 0.5417 (ptm-80) REVERT: E 239 ARG cc_start: 0.6219 (ptm160) cc_final: 0.4521 (ptt180) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1424 time to fit residues: 21.5217 Evaluate side-chains 97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN C 152 GLN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.131467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.112054 restraints weight = 10753.057| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.20 r_work: 0.3004 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9705 Z= 0.172 Angle : 0.730 12.496 13290 Z= 0.353 Chirality : 0.051 0.156 1490 Planarity : 0.006 0.053 1620 Dihedral : 11.482 118.507 1795 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.86 % Allowed : 12.77 % Favored : 83.37 % 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 aren not related in a simple way. whole: -0.86 (0.26), residues: 1045 helix: 0.13 (0.54), residues: 95 sheet: -0.34 (0.23), residues: 395 loop : -0.79 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 140 TYR 0.012 0.002 TYR A 148 PHE 0.015 0.001 PHE B 221 TRP 0.006 0.001 TRP C 90 HIS 0.002 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9675) covalent geometry : angle 0.65983 (13205) SS BOND : bond 0.00329 ( 5) SS BOND : angle 0.85871 ( 10) hydrogen bonds : bond 0.04576 ( 290) hydrogen bonds : angle 5.73387 ( 1020) link_BETA1-4 : bond 0.00132 ( 10) link_BETA1-4 : angle 1.46865 ( 30) link_NAG-ASN : bond 0.00253 ( 15) link_NAG-ASN : angle 5.27601 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.372 Fit side-chains REVERT: A 56 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7424 (mtm-85) REVERT: A 103 ASP cc_start: 0.7654 (t70) cc_final: 0.7453 (t0) REVERT: A 205 ASN cc_start: 0.7667 (m-40) cc_final: 0.7322 (m-40) REVERT: A 239 ARG cc_start: 0.5813 (ptm160) cc_final: 0.4031 (ptt180) REVERT: B 47 LYS cc_start: 0.9049 (ptmt) cc_final: 0.8820 (ptmt) REVERT: B 56 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7300 (mtm-85) REVERT: B 107 LYS cc_start: 0.8841 (ptmt) cc_final: 0.8580 (ptmt) REVERT: B 140 ARG cc_start: 0.7580 (ttm-80) cc_final: 0.7307 (mtp180) REVERT: B 239 ARG cc_start: 0.5989 (ptm160) cc_final: 0.4245 (ptt180) REVERT: C 56 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7345 (mtm-85) REVERT: C 103 ASP cc_start: 0.7765 (t70) cc_final: 0.7283 (t0) REVERT: C 205 ASN cc_start: 0.7815 (m-40) cc_final: 0.7410 (m-40) REVERT: D 47 LYS cc_start: 0.8825 (ptpp) cc_final: 0.8532 (ptmt) REVERT: D 56 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6656 (mtt90) REVERT: D 103 ASP cc_start: 0.7802 (t70) cc_final: 0.7352 (t0) REVERT: D 212 LEU cc_start: 0.8624 (mt) cc_final: 0.8323 (mt) REVERT: D 239 ARG cc_start: 0.5736 (ptm160) cc_final: 0.5195 (ptm-80) REVERT: E 56 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7269 (mtm-85) REVERT: E 77 ASN cc_start: 0.8543 (m-40) cc_final: 0.8223 (m-40) REVERT: E 148 TYR cc_start: 0.8889 (m-80) cc_final: 0.8598 (m-80) REVERT: E 197 LYS cc_start: 0.7956 (ttmm) cc_final: 0.7528 (ttmt) REVERT: E 239 ARG cc_start: 0.6280 (ptm160) cc_final: 0.4338 (ptt180) outliers start: 39 outliers final: 23 residues processed: 159 average time/residue: 0.1368 time to fit residues: 27.9257 Evaluate side-chains 146 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 86 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.135944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120778 restraints weight = 10389.263| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.67 r_work: 0.3008 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9705 Z= 0.163 Angle : 0.696 13.666 13290 Z= 0.329 Chirality : 0.049 0.136 1490 Planarity : 0.005 0.045 1620 Dihedral : 11.377 118.565 1795 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 5.15 % Allowed : 13.96 % Favored : 80.89 % 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 aren not related in a simple way. whole: -1.12 (0.26), residues: 1045 helix: 0.15 (0.55), residues: 95 sheet: -0.85 (0.23), residues: 445 loop : -0.65 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 200 TYR 0.016 0.002 TYR B 45 PHE 0.010 0.001 PHE E 221 TRP 0.007 0.001 TRP C 90 HIS 0.002 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9675) covalent geometry : angle 0.61146 (13205) SS BOND : bond 0.00263 ( 5) SS BOND : angle 0.72234 ( 10) hydrogen bonds : bond 0.03904 ( 290) hydrogen bonds : angle 5.31857 ( 1020) link_BETA1-4 : bond 0.00223 ( 10) link_BETA1-4 : angle 1.39244 ( 30) link_NAG-ASN : bond 0.01098 ( 15) link_NAG-ASN : angle 5.63422 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7972 (t0) cc_final: 0.7407 (t0) REVERT: A 127 ASP cc_start: 0.8398 (t0) cc_final: 0.8048 (t0) REVERT: A 205 ASN cc_start: 0.7786 (m-40) cc_final: 0.7565 (m-40) REVERT: A 239 ARG cc_start: 0.5942 (ptm160) cc_final: 0.4266 (ptt180) REVERT: B 56 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7859 (mtm-85) REVERT: B 78 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8291 (mm-40) REVERT: B 101 ASP cc_start: 0.8249 (t0) cc_final: 0.7963 (t0) REVERT: B 103 ASP cc_start: 0.7672 (t0) cc_final: 0.7444 (t0) REVERT: B 239 ARG cc_start: 0.6264 (ptm160) cc_final: 0.4712 (ptt180) REVERT: C 56 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7556 (mtm-85) REVERT: C 103 ASP cc_start: 0.7734 (t70) cc_final: 0.7433 (t0) REVERT: C 239 ARG cc_start: 0.6125 (ptm160) cc_final: 0.4528 (ptt180) REVERT: D 56 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7440 (mtm-85) REVERT: D 64 ASP cc_start: 0.9030 (t0) cc_final: 0.8795 (t70) REVERT: D 103 ASP cc_start: 0.7599 (t70) cc_final: 0.7316 (t0) REVERT: D 200 ARG cc_start: 0.8066 (mtp-110) cc_final: 0.7707 (mtp-110) REVERT: D 205 ASN cc_start: 0.7799 (m-40) cc_final: 0.7318 (m-40) REVERT: D 212 LEU cc_start: 0.8596 (mt) cc_final: 0.8376 (mt) REVERT: D 239 ARG cc_start: 0.5852 (ptm160) cc_final: 0.5450 (ptm-80) REVERT: E 101 ASP cc_start: 0.8081 (t0) cc_final: 0.7686 (t0) REVERT: E 239 ARG cc_start: 0.6457 (ptm160) cc_final: 0.4619 (ptt180) outliers start: 52 outliers final: 31 residues processed: 192 average time/residue: 0.1196 time to fit residues: 30.2954 Evaluate side-chains 172 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 138 TYR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 4 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN D 146 GLN E 146 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.126576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.108689 restraints weight = 10757.417| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.99 r_work: 0.2942 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9705 Z= 0.162 Angle : 0.688 13.029 13290 Z= 0.325 Chirality : 0.050 0.288 1490 Planarity : 0.005 0.040 1620 Dihedral : 11.299 116.237 1795 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.74 % Allowed : 14.46 % Favored : 79.80 % 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 aren not related in a simple way. whole: -1.20 (0.26), residues: 1045 helix: 0.10 (0.55), residues: 95 sheet: -0.96 (0.23), residues: 445 loop : -0.66 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 53 TYR 0.012 0.002 TYR B 45 PHE 0.012 0.001 PHE E 221 TRP 0.006 0.001 TRP D 55 HIS 0.002 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9675) covalent geometry : angle 0.61098 (13205) SS BOND : bond 0.00262 ( 5) SS BOND : angle 0.69271 ( 10) hydrogen bonds : bond 0.03395 ( 290) hydrogen bonds : angle 5.19722 ( 1020) link_BETA1-4 : bond 0.00199 ( 10) link_BETA1-4 : angle 1.37625 ( 30) link_NAG-ASN : bond 0.00699 ( 15) link_NAG-ASN : angle 5.37107 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 136 time to evaluate : 0.359 Fit side-chains REVERT: A 239 ARG cc_start: 0.5759 (ptm160) cc_final: 0.3963 (ptt180) REVERT: B 78 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8091 (mm-40) REVERT: B 101 ASP cc_start: 0.8249 (t0) cc_final: 0.7993 (t0) REVERT: B 103 ASP cc_start: 0.7795 (t0) cc_final: 0.7300 (t0) REVERT: B 107 LYS cc_start: 0.9053 (ptmt) cc_final: 0.8234 (ptmt) REVERT: B 239 ARG cc_start: 0.5950 (ptm160) cc_final: 0.4239 (ptt180) REVERT: C 56 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7742 (mtm-85) REVERT: C 103 ASP cc_start: 0.7793 (t70) cc_final: 0.7346 (t0) REVERT: C 239 ARG cc_start: 0.5981 (ptm160) cc_final: 0.4321 (ptt180) REVERT: D 56 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7611 (mtm-85) REVERT: D 101 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.8007 (t0) REVERT: D 103 ASP cc_start: 0.7660 (t70) cc_final: 0.7279 (t0) REVERT: D 108 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8433 (pt) REVERT: D 200 ARG cc_start: 0.7922 (mtp-110) cc_final: 0.7534 (mtp-110) REVERT: D 205 ASN cc_start: 0.7692 (m-40) cc_final: 0.7229 (m-40) REVERT: D 212 LEU cc_start: 0.8514 (mt) cc_final: 0.8287 (mt) REVERT: D 233 LYS cc_start: 0.8572 (mtpt) cc_final: 0.8358 (mtpp) REVERT: D 239 ARG cc_start: 0.5513 (ptm160) cc_final: 0.3831 (ptt180) REVERT: E 39 ASP cc_start: 0.8085 (m-30) cc_final: 0.7729 (m-30) REVERT: E 64 ASP cc_start: 0.9008 (t70) cc_final: 0.8371 (t0) REVERT: E 103 ASP cc_start: 0.7691 (t0) cc_final: 0.7369 (t0) REVERT: E 197 LYS cc_start: 0.7762 (ttmm) cc_final: 0.7177 (mtmt) REVERT: E 239 ARG cc_start: 0.5946 (ptm160) cc_final: 0.4100 (ptt180) outliers start: 58 outliers final: 40 residues processed: 186 average time/residue: 0.1154 time to fit residues: 28.3076 Evaluate side-chains 172 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 89 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.124315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.106426 restraints weight = 10836.720| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.00 r_work: 0.2970 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9705 Z= 0.120 Angle : 0.654 12.293 13290 Z= 0.305 Chirality : 0.048 0.183 1490 Planarity : 0.004 0.036 1620 Dihedral : 11.246 116.150 1795 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.65 % Allowed : 15.15 % Favored : 80.20 % 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 aren not related in a simple way. whole: -1.13 (0.27), residues: 1045 helix: 0.31 (0.56), residues: 95 sheet: -0.98 (0.23), residues: 445 loop : -0.58 (0.31), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 53 TYR 0.011 0.001 TYR B 45 PHE 0.010 0.001 PHE C 166 TRP 0.006 0.001 TRP C 90 HIS 0.002 0.000 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9675) covalent geometry : angle 0.57888 (13205) SS BOND : bond 0.00232 ( 5) SS BOND : angle 0.53205 ( 10) hydrogen bonds : bond 0.03077 ( 290) hydrogen bonds : angle 5.07025 ( 1020) link_BETA1-4 : bond 0.00281 ( 10) link_BETA1-4 : angle 1.21729 ( 30) link_NAG-ASN : bond 0.00670 ( 15) link_NAG-ASN : angle 5.17334 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 131 time to evaluate : 0.353 Fit side-chains REVERT: A 239 ARG cc_start: 0.5983 (ptm160) cc_final: 0.4223 (ptt180) REVERT: B 78 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8147 (mm-40) REVERT: B 101 ASP cc_start: 0.8266 (t0) cc_final: 0.7999 (t0) REVERT: B 103 ASP cc_start: 0.7800 (t0) cc_final: 0.7380 (t0) REVERT: B 107 LYS cc_start: 0.9147 (ptmt) cc_final: 0.8350 (ptmt) REVERT: B 239 ARG cc_start: 0.6063 (ptm160) cc_final: 0.4395 (ptt180) REVERT: C 56 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7908 (mtm-85) REVERT: C 103 ASP cc_start: 0.7748 (t70) cc_final: 0.7395 (t0) REVERT: C 200 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7431 (mtp-110) REVERT: C 239 ARG cc_start: 0.6033 (ptm160) cc_final: 0.4393 (ptt180) REVERT: D 56 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7868 (mtm-85) REVERT: D 101 ASP cc_start: 0.8193 (m-30) cc_final: 0.7960 (t0) REVERT: D 103 ASP cc_start: 0.7682 (t70) cc_final: 0.7301 (t0) REVERT: D 108 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8499 (pt) REVERT: D 239 ARG cc_start: 0.5620 (ptm160) cc_final: 0.3977 (ptt180) REVERT: E 197 LYS cc_start: 0.7798 (ttmm) cc_final: 0.7293 (mtmt) REVERT: E 239 ARG cc_start: 0.6264 (ptm160) cc_final: 0.4446 (ptt180) outliers start: 47 outliers final: 35 residues processed: 172 average time/residue: 0.1147 time to fit residues: 26.3482 Evaluate side-chains 165 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 7 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN C 146 GLN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN D 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.117182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.101436 restraints weight = 11205.474| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.79 r_work: 0.2926 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9705 Z= 0.182 Angle : 0.686 11.585 13290 Z= 0.324 Chirality : 0.049 0.159 1490 Planarity : 0.005 0.036 1620 Dihedral : 11.387 116.896 1795 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.45 % Allowed : 15.54 % Favored : 79.01 % 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 aren not related in a simple way. whole: -1.34 (0.27), residues: 1045 helix: 0.38 (0.56), residues: 95 sheet: -1.21 (0.22), residues: 480 loop : -0.58 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 53 TYR 0.012 0.002 TYR A 86 PHE 0.009 0.001 PHE C 164 TRP 0.007 0.001 TRP A 85 HIS 0.002 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9675) covalent geometry : angle 0.62197 (13205) SS BOND : bond 0.00238 ( 5) SS BOND : angle 0.89342 ( 10) hydrogen bonds : bond 0.03304 ( 290) hydrogen bonds : angle 5.11688 ( 1020) link_BETA1-4 : bond 0.00172 ( 10) link_BETA1-4 : angle 1.44162 ( 30) link_NAG-ASN : bond 0.00609 ( 15) link_NAG-ASN : angle 4.90182 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 144 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 239 ARG cc_start: 0.5896 (ptm160) cc_final: 0.4086 (ptt180) REVERT: B 78 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8117 (mm-40) REVERT: B 101 ASP cc_start: 0.8311 (t0) cc_final: 0.7867 (m-30) REVERT: B 103 ASP cc_start: 0.7813 (t0) cc_final: 0.7339 (t0) REVERT: B 107 LYS cc_start: 0.8993 (ptmt) cc_final: 0.8181 (ptmt) REVERT: B 239 ARG cc_start: 0.5943 (ptm160) cc_final: 0.4241 (ptt180) REVERT: C 56 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7940 (mtm-85) REVERT: C 103 ASP cc_start: 0.7751 (t70) cc_final: 0.7488 (t0) REVERT: C 166 PHE cc_start: 0.8152 (m-80) cc_final: 0.7939 (m-80) REVERT: C 197 LYS cc_start: 0.7511 (ttmm) cc_final: 0.7188 (ttmt) REVERT: C 220 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7903 (mt-10) REVERT: C 239 ARG cc_start: 0.5781 (ptm160) cc_final: 0.4203 (ptt180) REVERT: D 56 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7985 (mtm-85) REVERT: D 101 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7972 (t0) REVERT: D 103 ASP cc_start: 0.7656 (t70) cc_final: 0.7331 (t0) REVERT: D 108 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8383 (pt) REVERT: D 223 MET cc_start: 0.8606 (mmm) cc_final: 0.8355 (mmm) REVERT: D 239 ARG cc_start: 0.5348 (ptm160) cc_final: 0.3739 (ptt180) REVERT: E 103 ASP cc_start: 0.7540 (t0) cc_final: 0.7213 (t0) REVERT: E 197 LYS cc_start: 0.7818 (ttmm) cc_final: 0.7283 (mtmt) REVERT: E 220 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8088 (mt-10) REVERT: E 239 ARG cc_start: 0.5912 (ptm160) cc_final: 0.4098 (ptt180) outliers start: 55 outliers final: 47 residues processed: 191 average time/residue: 0.1185 time to fit residues: 30.2795 Evaluate side-chains 191 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 238 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 76 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.119870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.104688 restraints weight = 10994.955| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.70 r_work: 0.2983 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9705 Z= 0.114 Angle : 0.646 10.775 13290 Z= 0.303 Chirality : 0.047 0.135 1490 Planarity : 0.004 0.035 1620 Dihedral : 11.287 116.039 1795 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.06 % Allowed : 17.72 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.27), residues: 1045 helix: -0.81 (0.47), residues: 125 sheet: -1.27 (0.22), residues: 485 loop : -0.48 (0.33), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 53 TYR 0.020 0.001 TYR D 45 PHE 0.012 0.001 PHE E 221 TRP 0.006 0.001 TRP C 55 HIS 0.001 0.000 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9675) covalent geometry : angle 0.58607 (13205) SS BOND : bond 0.00217 ( 5) SS BOND : angle 0.53319 ( 10) hydrogen bonds : bond 0.02924 ( 290) hydrogen bonds : angle 5.00396 ( 1020) link_BETA1-4 : bond 0.00311 ( 10) link_BETA1-4 : angle 1.22978 ( 30) link_NAG-ASN : bond 0.00554 ( 15) link_NAG-ASN : angle 4.63565 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.418 Fit side-chains REVERT: A 134 ILE cc_start: 0.8445 (mm) cc_final: 0.8169 (mm) REVERT: A 239 ARG cc_start: 0.5882 (ptm160) cc_final: 0.4153 (ptt180) REVERT: B 78 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8076 (mm-40) REVERT: B 101 ASP cc_start: 0.8298 (t0) cc_final: 0.8017 (t0) REVERT: B 103 ASP cc_start: 0.7788 (t0) cc_final: 0.7388 (t0) REVERT: B 107 LYS cc_start: 0.8972 (ptmt) cc_final: 0.8161 (ptmt) REVERT: B 239 ARG cc_start: 0.5785 (ptm160) cc_final: 0.4233 (ptt180) REVERT: C 103 ASP cc_start: 0.7758 (t70) cc_final: 0.7424 (t0) REVERT: C 239 ARG cc_start: 0.5754 (ptm160) cc_final: 0.4214 (ptt180) REVERT: D 56 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7969 (mtm-85) REVERT: D 74 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6964 (m-30) REVERT: D 101 ASP cc_start: 0.8247 (m-30) cc_final: 0.7983 (t0) REVERT: D 103 ASP cc_start: 0.7612 (t70) cc_final: 0.7247 (t0) REVERT: D 108 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8440 (pt) REVERT: D 223 MET cc_start: 0.8558 (mmm) cc_final: 0.8331 (mmm) REVERT: D 239 ARG cc_start: 0.5495 (ptm160) cc_final: 0.3902 (ptt180) REVERT: E 78 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8154 (mm-40) REVERT: E 103 ASP cc_start: 0.7593 (t0) cc_final: 0.7230 (t0) REVERT: E 197 LYS cc_start: 0.7781 (ttmm) cc_final: 0.7239 (mtmt) REVERT: E 220 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7955 (mt-10) REVERT: E 239 ARG cc_start: 0.5877 (ptm160) cc_final: 0.4065 (ptt180) outliers start: 41 outliers final: 33 residues processed: 170 average time/residue: 0.1214 time to fit residues: 27.3989 Evaluate side-chains 170 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN D 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.115414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.099983 restraints weight = 11219.404| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.77 r_work: 0.2908 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9705 Z= 0.198 Angle : 0.683 10.178 13290 Z= 0.326 Chirality : 0.049 0.139 1490 Planarity : 0.005 0.033 1620 Dihedral : 11.460 117.306 1795 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.35 % Allowed : 16.44 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.26), residues: 1045 helix: -0.85 (0.47), residues: 125 sheet: -1.31 (0.22), residues: 480 loop : -0.68 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 200 TYR 0.022 0.002 TYR D 45 PHE 0.011 0.001 PHE E 221 TRP 0.008 0.001 TRP C 85 HIS 0.001 0.001 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9675) covalent geometry : angle 0.62855 (13205) SS BOND : bond 0.00245 ( 5) SS BOND : angle 1.00069 ( 10) hydrogen bonds : bond 0.03308 ( 290) hydrogen bonds : angle 5.07180 ( 1020) link_BETA1-4 : bond 0.00159 ( 10) link_BETA1-4 : angle 1.50712 ( 30) link_NAG-ASN : bond 0.00581 ( 15) link_NAG-ASN : angle 4.47129 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 151 time to evaluate : 0.372 Fit side-chains REVERT: A 239 ARG cc_start: 0.5787 (ptm160) cc_final: 0.3967 (ptt180) REVERT: B 78 GLN cc_start: 0.8305 (mm-40) cc_final: 0.8066 (mm-40) REVERT: B 101 ASP cc_start: 0.8321 (t0) cc_final: 0.7917 (m-30) REVERT: B 103 ASP cc_start: 0.7913 (t0) cc_final: 0.7509 (t0) REVERT: B 107 LYS cc_start: 0.8952 (ptmt) cc_final: 0.8146 (ptmt) REVERT: B 239 ARG cc_start: 0.5788 (ptm160) cc_final: 0.4151 (ptt180) REVERT: C 103 ASP cc_start: 0.7743 (t70) cc_final: 0.7486 (t0) REVERT: C 197 LYS cc_start: 0.7416 (ttmm) cc_final: 0.7103 (ttmt) REVERT: C 239 ARG cc_start: 0.5786 (ptm160) cc_final: 0.4093 (ptt180) REVERT: D 56 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7939 (mtm-85) REVERT: D 101 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7987 (t0) REVERT: D 103 ASP cc_start: 0.7696 (t70) cc_final: 0.7364 (t0) REVERT: D 108 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8374 (pt) REVERT: D 134 ILE cc_start: 0.8378 (mm) cc_final: 0.8080 (mm) REVERT: D 182 ILE cc_start: 0.8858 (tt) cc_final: 0.8561 (tt) REVERT: D 200 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7285 (mtp-110) REVERT: D 223 MET cc_start: 0.8611 (mmm) cc_final: 0.8358 (mmm) REVERT: D 239 ARG cc_start: 0.5337 (ptm160) cc_final: 0.3734 (ptt180) REVERT: E 197 LYS cc_start: 0.7812 (ttmm) cc_final: 0.7273 (mtmt) REVERT: E 220 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8241 (mt-10) REVERT: E 239 ARG cc_start: 0.5920 (ptm160) cc_final: 0.4056 (ptt180) outliers start: 54 outliers final: 48 residues processed: 196 average time/residue: 0.0971 time to fit residues: 25.4792 Evaluate side-chains 198 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 238 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 76 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 205 ASN C 206 GLN D 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.121657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.103183 restraints weight = 10998.858| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.11 r_work: 0.2914 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9705 Z= 0.131 Angle : 0.632 9.384 13290 Z= 0.301 Chirality : 0.048 0.134 1490 Planarity : 0.004 0.033 1620 Dihedral : 11.375 116.833 1795 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.75 % Allowed : 17.92 % Favored : 77.33 % 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 aren not related in a simple way. whole: -1.60 (0.27), residues: 1045 helix: -0.80 (0.47), residues: 125 sheet: -1.35 (0.23), residues: 475 loop : -0.54 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 53 TYR 0.018 0.001 TYR D 45 PHE 0.009 0.001 PHE E 221 TRP 0.007 0.001 TRP C 90 HIS 0.001 0.000 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9675) covalent geometry : angle 0.58292 (13205) SS BOND : bond 0.00231 ( 5) SS BOND : angle 0.61306 ( 10) hydrogen bonds : bond 0.02947 ( 290) hydrogen bonds : angle 4.94633 ( 1020) link_BETA1-4 : bond 0.00279 ( 10) link_BETA1-4 : angle 1.28178 ( 30) link_NAG-ASN : bond 0.00505 ( 15) link_NAG-ASN : angle 4.15009 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 239 ARG cc_start: 0.5992 (ptm160) cc_final: 0.4178 (ptt180) REVERT: B 78 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8135 (mm-40) REVERT: B 101 ASP cc_start: 0.8356 (t0) cc_final: 0.7935 (m-30) REVERT: B 103 ASP cc_start: 0.7978 (t0) cc_final: 0.7551 (t0) REVERT: B 107 LYS cc_start: 0.9003 (ptmt) cc_final: 0.8246 (ptmt) REVERT: B 220 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7949 (mt-10) REVERT: B 239 ARG cc_start: 0.5886 (ptm160) cc_final: 0.4335 (ptt180) REVERT: C 103 ASP cc_start: 0.7822 (t70) cc_final: 0.7530 (t0) REVERT: C 205 ASN cc_start: 0.7993 (OUTLIER) cc_final: 0.7669 (m-40) REVERT: C 239 ARG cc_start: 0.5883 (ptm160) cc_final: 0.4263 (ptt180) REVERT: D 56 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.8022 (mtm-85) REVERT: D 101 ASP cc_start: 0.8267 (m-30) cc_final: 0.8012 (t0) REVERT: D 103 ASP cc_start: 0.7784 (t70) cc_final: 0.7463 (t0) REVERT: D 108 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8460 (pt) REVERT: D 223 MET cc_start: 0.8614 (mmm) cc_final: 0.8382 (mmm) REVERT: D 239 ARG cc_start: 0.5557 (ptm160) cc_final: 0.4014 (ptt180) REVERT: E 78 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8165 (mm-40) REVERT: E 103 ASP cc_start: 0.7630 (t0) cc_final: 0.7402 (t0) REVERT: E 197 LYS cc_start: 0.7766 (ttmm) cc_final: 0.7232 (mtmt) REVERT: E 220 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8180 (mt-10) REVERT: E 239 ARG cc_start: 0.6025 (ptm160) cc_final: 0.4197 (ptt180) outliers start: 48 outliers final: 43 residues processed: 181 average time/residue: 0.1081 time to fit residues: 26.3498 Evaluate side-chains 183 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 238 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 8 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 0.0570 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 205 ASN D 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.120071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.101320 restraints weight = 11074.304| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.16 r_work: 0.2931 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9705 Z= 0.128 Angle : 0.629 9.092 13290 Z= 0.300 Chirality : 0.047 0.134 1490 Planarity : 0.004 0.033 1620 Dihedral : 11.343 116.624 1795 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.65 % Allowed : 18.02 % Favored : 77.33 % 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 aren not related in a simple way. whole: -1.69 (0.27), residues: 1045 helix: -0.79 (0.47), residues: 125 sheet: -1.50 (0.23), residues: 490 loop : -0.42 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 53 TYR 0.017 0.001 TYR D 45 PHE 0.009 0.001 PHE E 221 TRP 0.008 0.001 TRP C 90 HIS 0.002 0.000 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9675) covalent geometry : angle 0.58096 (13205) SS BOND : bond 0.00202 ( 5) SS BOND : angle 0.57429 ( 10) hydrogen bonds : bond 0.02918 ( 290) hydrogen bonds : angle 4.91342 ( 1020) link_BETA1-4 : bond 0.00284 ( 10) link_BETA1-4 : angle 1.29744 ( 30) link_NAG-ASN : bond 0.00503 ( 15) link_NAG-ASN : angle 4.05372 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 239 ARG cc_start: 0.5949 (ptm160) cc_final: 0.4151 (ptt180) REVERT: B 78 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8098 (mm-40) REVERT: B 101 ASP cc_start: 0.8347 (t0) cc_final: 0.7923 (m-30) REVERT: B 103 ASP cc_start: 0.7966 (t0) cc_final: 0.7579 (t0) REVERT: B 107 LYS cc_start: 0.9024 (ptmt) cc_final: 0.8260 (ptmt) REVERT: B 239 ARG cc_start: 0.5870 (ptm160) cc_final: 0.4293 (ptt180) REVERT: C 103 ASP cc_start: 0.7821 (t70) cc_final: 0.7529 (t0) REVERT: C 239 ARG cc_start: 0.5840 (ptm160) cc_final: 0.4235 (ptt180) REVERT: D 56 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.8001 (mtm-85) REVERT: D 101 ASP cc_start: 0.8257 (m-30) cc_final: 0.8005 (t0) REVERT: D 103 ASP cc_start: 0.7721 (t70) cc_final: 0.7390 (t0) REVERT: D 108 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8445 (pt) REVERT: D 223 MET cc_start: 0.8605 (mmm) cc_final: 0.8368 (mmm) REVERT: D 239 ARG cc_start: 0.5601 (ptm160) cc_final: 0.4044 (ptt180) REVERT: D 241 ARG cc_start: 0.7965 (ptt180) cc_final: 0.7523 (ptt180) REVERT: E 78 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8138 (mm-40) REVERT: E 197 LYS cc_start: 0.7781 (ttmm) cc_final: 0.7245 (mtmt) REVERT: E 220 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8203 (mt-10) REVERT: E 239 ARG cc_start: 0.6021 (ptm160) cc_final: 0.4167 (ptt180) outliers start: 47 outliers final: 42 residues processed: 183 average time/residue: 0.1148 time to fit residues: 27.7702 Evaluate side-chains 185 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 238 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 205 ASN D 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.118526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.100534 restraints weight = 11053.963| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.06 r_work: 0.2955 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9705 Z= 0.144 Angle : 0.630 8.383 13290 Z= 0.303 Chirality : 0.048 0.135 1490 Planarity : 0.004 0.033 1620 Dihedral : 11.331 116.890 1795 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.55 % Allowed : 18.42 % Favored : 77.03 % 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 aren not related in a simple way. whole: -1.64 (0.26), residues: 1045 helix: -0.79 (0.47), residues: 125 sheet: -1.35 (0.24), residues: 440 loop : -0.69 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 53 TYR 0.027 0.001 TYR D 45 PHE 0.008 0.001 PHE E 221 TRP 0.008 0.001 TRP A 85 HIS 0.001 0.000 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9675) covalent geometry : angle 0.58681 (13205) SS BOND : bond 0.00222 ( 5) SS BOND : angle 0.72754 ( 10) hydrogen bonds : bond 0.02972 ( 290) hydrogen bonds : angle 4.91601 ( 1020) link_BETA1-4 : bond 0.00241 ( 10) link_BETA1-4 : angle 1.35080 ( 30) link_NAG-ASN : bond 0.00484 ( 15) link_NAG-ASN : angle 3.82850 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2109.25 seconds wall clock time: 36 minutes 47.14 seconds (2207.14 seconds total)