Starting phenix.real_space_refine on Thu Sep 18 16:46:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s5e_19733/09_2025/8s5e_19733_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s5e_19733/09_2025/8s5e_19733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8s5e_19733/09_2025/8s5e_19733_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s5e_19733/09_2025/8s5e_19733_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s5e_19733/09_2025/8s5e_19733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s5e_19733/09_2025/8s5e_19733.map" } resolution = 3.1 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= -0.308 sd= 5.853 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: 7 Type Number sf(0) Gaussians P 21 5.49 5 Mg 7 5.21 5 S 49 5.16 5 C 5852 2.51 5 N 1645 2.21 5 O 1799 1.98 5 H 9135 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18508 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 2609 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 2609 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 2609 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 2609 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 2609 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 2609 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 2609 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.65, per 1000 atoms: 0.20 Number of scatterers: 18508 At special positions: 0 Unit cell: (88.7638, 111.72, 123.963, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 49 16.00 P 21 15.00 Mg 7 11.99 O 1799 8.00 N 1645 7.00 C 5852 6.00 H 9135 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 804.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 30.8% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 29 through 38 Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.562A pdb=" N TYR A 82 " --> pdb=" O TRP A 78 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 83' Processing helix chain 'A' and resid 99 through 111 Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.612A pdb=" N LEU A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 171 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'B' and resid 29 through 38 Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.562A pdb=" N TYR B 82 " --> pdb=" O TRP B 78 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG B 83 " --> pdb=" O ARG B 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 78 through 83' Processing helix chain 'B' and resid 99 through 111 Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.612A pdb=" N LEU B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 171 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'C' and resid 29 through 38 Processing helix chain 'C' and resid 78 through 83 removed outlier: 3.562A pdb=" N TYR C 82 " --> pdb=" O TRP C 78 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 83' Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'C' and resid 135 through 143 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.613A pdb=" N LEU C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 171 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'D' and resid 29 through 38 Processing helix chain 'D' and resid 78 through 83 removed outlier: 3.562A pdb=" N TYR D 82 " --> pdb=" O TRP D 78 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 83' Processing helix chain 'D' and resid 99 through 111 Processing helix chain 'D' and resid 135 through 143 Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.612A pdb=" N LEU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 171 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'E' and resid 29 through 38 Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.562A pdb=" N TYR E 82 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 83' Processing helix chain 'E' and resid 99 through 111 Processing helix chain 'E' and resid 135 through 143 Processing helix chain 'E' and resid 166 through 174 removed outlier: 3.612A pdb=" N LEU E 170 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU E 171 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'F' and resid 29 through 38 Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.562A pdb=" N TYR F 82 " --> pdb=" O TRP F 78 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG F 83 " --> pdb=" O ARG F 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 78 through 83' Processing helix chain 'F' and resid 99 through 111 Processing helix chain 'F' and resid 135 through 143 Processing helix chain 'F' and resid 166 through 174 removed outlier: 3.613A pdb=" N LEU F 170 " --> pdb=" O LEU F 166 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU F 171 " --> pdb=" O TYR F 167 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'G' and resid 29 through 39 removed outlier: 3.550A pdb=" N LEU G 39 " --> pdb=" O TYR G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.562A pdb=" N TYR G 82 " --> pdb=" O TRP G 78 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 78 through 83' Processing helix chain 'G' and resid 99 through 111 Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 166 through 174 removed outlier: 3.613A pdb=" N LEU G 170 " --> pdb=" O LEU G 166 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU G 171 " --> pdb=" O TYR G 167 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 58 removed outlier: 3.717A pdb=" N VAL A 68 " --> pdb=" O MET A 22 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY A 24 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG A 19 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE A 89 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 21 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL A 91 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 23 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ASP A 93 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP A 121 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN A 156 " --> pdb=" O TRP A 121 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL A 123 " --> pdb=" O GLN A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 58 removed outlier: 3.717A pdb=" N VAL B 68 " --> pdb=" O MET B 22 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY B 24 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG B 19 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE B 89 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 21 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL B 91 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 23 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ASP B 93 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP B 121 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN B 156 " --> pdb=" O TRP B 121 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL B 123 " --> pdb=" O GLN B 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 58 removed outlier: 3.717A pdb=" N VAL C 68 " --> pdb=" O MET C 22 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY C 24 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG C 19 " --> pdb=" O GLY C 87 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE C 89 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C 21 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL C 91 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL C 23 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ASP C 93 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP C 121 " --> pdb=" O PHE C 154 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN C 156 " --> pdb=" O TRP C 121 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL C 123 " --> pdb=" O GLN C 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 58 removed outlier: 3.717A pdb=" N VAL D 68 " --> pdb=" O MET D 22 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY D 24 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG D 19 " --> pdb=" O GLY D 87 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE D 89 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU D 21 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL D 91 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 23 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ASP D 93 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP D 121 " --> pdb=" O PHE D 154 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLN D 156 " --> pdb=" O TRP D 121 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL D 123 " --> pdb=" O GLN D 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 51 through 58 removed outlier: 3.718A pdb=" N VAL E 68 " --> pdb=" O MET E 22 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY E 24 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG E 19 " --> pdb=" O GLY E 87 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE E 89 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU E 21 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL E 91 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL E 23 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ASP E 93 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP E 121 " --> pdb=" O PHE E 154 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN E 156 " --> pdb=" O TRP E 121 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL E 123 " --> pdb=" O GLN E 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 51 through 58 removed outlier: 3.717A pdb=" N VAL F 68 " --> pdb=" O MET F 22 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY F 24 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARG F 19 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE F 89 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU F 21 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL F 91 " --> pdb=" O LEU F 21 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL F 23 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ASP F 93 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP F 121 " --> pdb=" O PHE F 154 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN F 156 " --> pdb=" O TRP F 121 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL F 123 " --> pdb=" O GLN F 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 51 through 58 removed outlier: 3.716A pdb=" N VAL G 68 " --> pdb=" O MET G 22 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY G 24 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG G 19 " --> pdb=" O GLY G 87 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE G 89 " --> pdb=" O ARG G 19 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU G 21 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL G 91 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL G 23 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ASP G 93 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP G 121 " --> pdb=" O PHE G 154 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN G 156 " --> pdb=" O TRP G 121 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL G 123 " --> pdb=" O GLN G 156 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 9128 1.04 - 1.25: 1533 1.25 - 1.47: 3836 1.47 - 1.68: 4088 1.68 - 1.89: 84 Bond restraints: 18669 Sorted by residual: bond pdb=" C3' GSP D 202 " pdb=" C4' GSP D 202 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C3' GSP G 202 " pdb=" C4' GSP G 202 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3' GSP C 202 " pdb=" C4' GSP C 202 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3' GSP A 202 " pdb=" C4' GSP A 202 " ideal model delta sigma weight residual 1.524 1.300 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3' GSP F 202 " pdb=" C4' GSP F 202 " ideal model delta sigma weight residual 1.524 1.300 0.224 2.00e-02 2.50e+03 1.26e+02 ... (remaining 18664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 33484 3.54 - 7.09: 88 7.09 - 10.63: 7 10.63 - 14.17: 0 14.17 - 17.72: 14 Bond angle restraints: 33593 Sorted by residual: angle pdb=" C1' GSP D 202 " pdb=" N9 GSP D 202 " pdb=" C4 GSP D 202 " ideal model delta sigma weight residual 126.00 108.28 17.72 3.00e+00 1.11e-01 3.49e+01 angle pdb=" C1' GSP G 202 " pdb=" N9 GSP G 202 " pdb=" C4 GSP G 202 " ideal model delta sigma weight residual 126.00 108.30 17.70 3.00e+00 1.11e-01 3.48e+01 angle pdb=" C1' GSP E 202 " pdb=" N9 GSP E 202 " pdb=" C4 GSP E 202 " ideal model delta sigma weight residual 126.00 108.30 17.70 3.00e+00 1.11e-01 3.48e+01 angle pdb=" C1' GSP C 202 " pdb=" N9 GSP C 202 " pdb=" C4 GSP C 202 " ideal model delta sigma weight residual 126.00 108.31 17.69 3.00e+00 1.11e-01 3.48e+01 angle pdb=" C1' GSP F 202 " pdb=" N9 GSP F 202 " pdb=" C4 GSP F 202 " ideal model delta sigma weight residual 126.00 108.32 17.68 3.00e+00 1.11e-01 3.47e+01 ... (remaining 33588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 7884 21.99 - 43.99: 571 43.99 - 65.98: 126 65.98 - 87.98: 22 87.98 - 109.97: 14 Dihedral angle restraints: 8617 sinusoidal: 4781 harmonic: 3836 Sorted by residual: dihedral pdb=" O2G GSP E 202 " pdb=" O3B GSP E 202 " pdb=" PG GSP E 202 " pdb=" PB GSP E 202 " ideal model delta sinusoidal sigma weight residual 70.94 -39.03 109.97 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" O2G GSP A 202 " pdb=" O3B GSP A 202 " pdb=" PG GSP A 202 " pdb=" PB GSP A 202 " ideal model delta sinusoidal sigma weight residual 70.94 -39.03 109.97 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" O2G GSP B 202 " pdb=" O3B GSP B 202 " pdb=" PG GSP B 202 " pdb=" PB GSP B 202 " ideal model delta sinusoidal sigma weight residual 70.94 -39.01 109.96 1 2.00e+01 2.50e-03 3.22e+01 ... (remaining 8614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 529 0.027 - 0.053: 420 0.053 - 0.079: 301 0.079 - 0.106: 135 0.106 - 0.132: 43 Chirality restraints: 1428 Sorted by residual: chirality pdb=" CA ILE F 46 " pdb=" N ILE F 46 " pdb=" C ILE F 46 " pdb=" CB ILE F 46 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE A 46 " pdb=" N ILE A 46 " pdb=" C ILE A 46 " pdb=" CB ILE A 46 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1425 not shown) Planarity restraints: 2716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 57 " 0.208 2.00e-02 2.50e+03 4.08e-01 2.50e+03 pdb=" CD GLN E 57 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN E 57 " -0.205 2.00e-02 2.50e+03 pdb=" NE2 GLN E 57 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN E 57 " -0.671 2.00e-02 2.50e+03 pdb="HE22 GLN E 57 " 0.681 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 57 " 0.252 2.00e-02 2.50e+03 3.26e-01 1.60e+03 pdb=" CD GLN G 57 " -0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN G 57 " -0.247 2.00e-02 2.50e+03 pdb=" NE2 GLN G 57 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN G 57 " -0.503 2.00e-02 2.50e+03 pdb="HE22 GLN G 57 " 0.511 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 57 " -0.240 2.00e-02 2.50e+03 2.97e-01 1.33e+03 pdb=" CD GLN F 57 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN F 57 " 0.239 2.00e-02 2.50e+03 pdb=" NE2 GLN F 57 " -0.008 2.00e-02 2.50e+03 pdb="HE21 GLN F 57 " 0.453 2.00e-02 2.50e+03 pdb="HE22 GLN F 57 " -0.459 2.00e-02 2.50e+03 ... (remaining 2713 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 317 2.08 - 2.71: 30944 2.71 - 3.34: 51238 3.34 - 3.97: 68065 3.97 - 4.60: 110885 Nonbonded interactions: 261449 Sorted by model distance: nonbonded pdb=" HG1 THR B 48 " pdb="MG MG B 201 " model vdw 1.447 1.700 nonbonded pdb=" HG1 THR D 48 " pdb="MG MG D 201 " model vdw 1.447 1.700 nonbonded pdb=" HG1 THR F 48 " pdb="MG MG F 201 " model vdw 1.448 1.700 nonbonded pdb=" HG1 THR C 48 " pdb="MG MG C 201 " model vdw 1.448 1.700 nonbonded pdb=" HG1 THR E 48 " pdb="MG MG E 201 " model vdw 1.448 1.700 ... (remaining 261444 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 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: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.910 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 0.017 0.225 9534 Z= 0.776 Angle : 0.991 17.717 12943 Z= 0.482 Chirality : 0.052 0.132 1428 Planarity : 0.005 0.042 1603 Dihedral : 16.828 109.972 3528 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.21 % Allowed : 10.89 % Favored : 84.89 % 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: -1.35 (0.26), residues: 1127 helix: -2.33 (0.26), residues: 294 sheet: -1.70 (0.25), residues: 308 loop : 0.87 (0.31), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 109 TYR 0.007 0.001 TYR B 35 PHE 0.011 0.002 PHE F 154 TRP 0.009 0.002 TRP F 153 HIS 0.002 0.001 HIS E 80 Details of bonding type rmsd covalent geometry : bond 0.01678 ( 9534) covalent geometry : angle 0.99079 (12943) hydrogen bonds : bond 0.15444 ( 287) hydrogen bonds : angle 6.09332 ( 819) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 258 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7860 (mp) REVERT: A 171 GLU cc_start: 0.8456 (tp30) cc_final: 0.8047 (tt0) REVERT: B 41 GLU cc_start: 0.8311 (pt0) cc_final: 0.8051 (pt0) REVERT: B 49 ILE cc_start: 0.9108 (mm) cc_final: 0.8877 (mt) REVERT: B 52 ASN cc_start: 0.8614 (m-40) cc_final: 0.8372 (m110) REVERT: B 108 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7681 (mm110) REVERT: B 113 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8012 (mm-30) REVERT: B 126 ASN cc_start: 0.8900 (t0) cc_final: 0.8666 (t0) REVERT: B 149 ARG cc_start: 0.8996 (ptt-90) cc_final: 0.8775 (ptt-90) REVERT: B 150 ASN cc_start: 0.8214 (p0) cc_final: 0.7863 (p0) REVERT: C 45 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7803 (p) REVERT: C 59 LYS cc_start: 0.7678 (mtpp) cc_final: 0.7467 (mtpt) REVERT: C 67 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7918 (t0) REVERT: C 71 GLN cc_start: 0.8469 (mt0) cc_final: 0.8265 (mt0) REVERT: C 83 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7614 (ttp80) REVERT: C 97 ARG cc_start: 0.8508 (ttm110) cc_final: 0.8218 (ttm110) REVERT: C 107 MET cc_start: 0.9102 (ttp) cc_final: 0.8326 (ttp) REVERT: C 142 LYS cc_start: 0.8973 (mttp) cc_final: 0.8583 (mmtm) REVERT: C 149 ARG cc_start: 0.9006 (ptt-90) cc_final: 0.7598 (ptm-80) REVERT: D 18 MET cc_start: 0.8625 (ttt) cc_final: 0.8186 (ttt) REVERT: D 46 ILE cc_start: 0.8846 (pt) cc_final: 0.8590 (pt) REVERT: D 107 MET cc_start: 0.8938 (ttp) cc_final: 0.8590 (ttp) REVERT: D 149 ARG cc_start: 0.8933 (ptt-90) cc_final: 0.7318 (ptm-80) REVERT: D 168 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8178 (mt-10) REVERT: E 18 MET cc_start: 0.8472 (ttt) cc_final: 0.8082 (ttt) REVERT: E 149 ARG cc_start: 0.8627 (ptt-90) cc_final: 0.7110 (ptm160) REVERT: E 168 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8078 (mt-10) REVERT: F 42 VAL cc_start: 0.8719 (t) cc_final: 0.8410 (p) REVERT: F 56 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8352 (m) REVERT: F 67 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7451 (t0) REVERT: F 79 ARG cc_start: 0.8302 (mtt-85) cc_final: 0.8064 (mtt-85) REVERT: F 96 ASP cc_start: 0.8437 (t70) cc_final: 0.8038 (t0) REVERT: F 110 MET cc_start: 0.9088 (ttp) cc_final: 0.8878 (ttm) REVERT: F 142 LYS cc_start: 0.8944 (mttp) cc_final: 0.8742 (mttm) REVERT: G 107 MET cc_start: 0.8877 (ttp) cc_final: 0.8539 (ttp) REVERT: G 114 ASP cc_start: 0.8464 (m-30) cc_final: 0.8210 (m-30) REVERT: G 126 ASN cc_start: 0.8866 (t0) cc_final: 0.8646 (t0) REVERT: G 138 GLU cc_start: 0.8148 (tt0) cc_final: 0.7806 (mt-10) outliers start: 41 outliers final: 17 residues processed: 287 average time/residue: 0.2849 time to fit residues: 105.9525 Evaluate side-chains 211 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 67 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.0980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 0.4980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 108 GLN C 118 ASN E 108 GLN E 156 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.090279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.077272 restraints weight = 36149.572| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 1.79 r_work: 0.2565 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2440 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9534 Z= 0.113 Angle : 0.527 6.771 12943 Z= 0.258 Chirality : 0.044 0.180 1428 Planarity : 0.004 0.043 1603 Dihedral : 6.978 53.315 1385 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.85 % Allowed : 13.98 % Favored : 84.17 % 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: 0.08 (0.28), residues: 1127 helix: -1.07 (0.29), residues: 294 sheet: -1.11 (0.26), residues: 308 loop : 1.91 (0.34), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 79 TYR 0.011 0.001 TYR E 35 PHE 0.008 0.001 PHE F 154 TRP 0.007 0.001 TRP E 66 HIS 0.002 0.000 HIS G 80 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9534) covalent geometry : angle 0.52650 (12943) hydrogen bonds : bond 0.03190 ( 287) hydrogen bonds : angle 4.29928 ( 819) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.9105 (tptp) cc_final: 0.8897 (tptm) REVERT: A 149 ARG cc_start: 0.9284 (ptt-90) cc_final: 0.8870 (ptt90) REVERT: A 171 GLU cc_start: 0.8721 (tp30) cc_final: 0.8448 (mm-30) REVERT: B 57 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8601 (mm-40) REVERT: B 113 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7792 (mm-30) REVERT: B 150 ASN cc_start: 0.8360 (p0) cc_final: 0.8028 (p0) REVERT: B 158 THR cc_start: 0.9125 (p) cc_final: 0.8710 (p) REVERT: C 45 THR cc_start: 0.8382 (p) cc_final: 0.8022 (p) REVERT: C 59 LYS cc_start: 0.7755 (mtpp) cc_final: 0.7491 (mtpt) REVERT: C 67 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8213 (t0) REVERT: C 71 GLN cc_start: 0.8618 (mt0) cc_final: 0.8369 (mt0) REVERT: C 83 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7768 (ttp80) REVERT: C 97 ARG cc_start: 0.8341 (ttm110) cc_final: 0.8009 (ttm170) REVERT: C 107 MET cc_start: 0.9256 (ttp) cc_final: 0.8779 (ttp) REVERT: C 149 ARG cc_start: 0.9044 (ptt-90) cc_final: 0.7608 (ptm-80) REVERT: C 171 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8397 (mm-30) REVERT: D 18 MET cc_start: 0.8634 (ttt) cc_final: 0.8231 (ttt) REVERT: D 26 ASP cc_start: 0.9228 (p0) cc_final: 0.9007 (p0) REVERT: D 83 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7792 (ttm-80) REVERT: D 107 MET cc_start: 0.9107 (ttp) cc_final: 0.8254 (ttp) REVERT: D 149 ARG cc_start: 0.9099 (ptt-90) cc_final: 0.7418 (ptm-80) REVERT: E 18 MET cc_start: 0.8562 (ttt) cc_final: 0.8184 (ttt) REVERT: E 149 ARG cc_start: 0.8841 (ptt-90) cc_final: 0.7217 (ptm160) REVERT: E 168 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8129 (mt-10) REVERT: F 56 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8312 (p) REVERT: F 67 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.7769 (t0) REVERT: F 79 ARG cc_start: 0.8206 (mtt-85) cc_final: 0.7912 (mtt-85) REVERT: F 96 ASP cc_start: 0.8345 (t70) cc_final: 0.7948 (t0) REVERT: F 161 THR cc_start: 0.8124 (p) cc_final: 0.7894 (p) REVERT: G 16 LYS cc_start: 0.7886 (tptt) cc_final: 0.7537 (tppt) REVERT: G 107 MET cc_start: 0.8974 (ttp) cc_final: 0.8740 (ttp) REVERT: G 108 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8208 (mm-40) REVERT: G 126 ASN cc_start: 0.8963 (t0) cc_final: 0.8741 (t0) REVERT: G 138 GLU cc_start: 0.8258 (tt0) cc_final: 0.7894 (tt0) REVERT: G 142 LYS cc_start: 0.8488 (mttp) cc_final: 0.8183 (mttp) outliers start: 18 outliers final: 11 residues processed: 202 average time/residue: 0.3264 time to fit residues: 82.4638 Evaluate side-chains 199 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 96 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN G 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.085361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.072572 restraints weight = 37568.721| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 1.75 r_work: 0.2499 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2376 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 9534 Z= 0.199 Angle : 0.574 8.079 12943 Z= 0.282 Chirality : 0.046 0.173 1428 Planarity : 0.004 0.043 1603 Dihedral : 6.290 38.106 1367 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.85 % Allowed : 14.59 % Favored : 83.56 % 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: 0.43 (0.28), residues: 1127 helix: -0.31 (0.30), residues: 294 sheet: -0.92 (0.26), residues: 322 loop : 1.90 (0.34), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 75 TYR 0.013 0.002 TYR E 35 PHE 0.023 0.002 PHE F 154 TRP 0.010 0.001 TRP G 172 HIS 0.004 0.001 HIS G 80 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 9534) covalent geometry : angle 0.57373 (12943) hydrogen bonds : bond 0.03536 ( 287) hydrogen bonds : angle 4.25572 ( 819) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.9079 (p0) cc_final: 0.8872 (p0) REVERT: A 171 GLU cc_start: 0.8777 (tp30) cc_final: 0.8407 (mm-30) REVERT: B 79 ARG cc_start: 0.8242 (mtt-85) cc_final: 0.7912 (mtt180) REVERT: B 83 ARG cc_start: 0.7578 (ttp80) cc_final: 0.7378 (ttp-170) REVERT: B 109 ARG cc_start: 0.8105 (ttm110) cc_final: 0.7701 (ttp80) REVERT: B 113 GLU cc_start: 0.8645 (mm-30) cc_final: 0.7856 (mm-30) REVERT: B 149 ARG cc_start: 0.9205 (ptt90) cc_final: 0.8795 (ptt-90) REVERT: C 83 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7999 (ttp80) REVERT: C 97 ARG cc_start: 0.8324 (ttm110) cc_final: 0.8062 (ttm110) REVERT: C 107 MET cc_start: 0.9295 (ttp) cc_final: 0.8866 (ttp) REVERT: C 149 ARG cc_start: 0.9017 (ptt-90) cc_final: 0.7414 (ptm-80) REVERT: C 171 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8498 (mm-30) REVERT: D 17 GLU cc_start: 0.8480 (tt0) cc_final: 0.7862 (tp30) REVERT: D 46 ILE cc_start: 0.8718 (pt) cc_final: 0.8468 (pt) REVERT: D 83 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8144 (ttm-80) REVERT: D 107 MET cc_start: 0.9008 (ttp) cc_final: 0.8004 (ttp) REVERT: D 129 ASP cc_start: 0.8829 (p0) cc_final: 0.8585 (p0) REVERT: D 149 ARG cc_start: 0.9078 (ptt-90) cc_final: 0.7322 (ptm-80) REVERT: E 16 LYS cc_start: 0.7356 (tptm) cc_final: 0.6949 (tptm) REVERT: E 18 MET cc_start: 0.8740 (ttt) cc_final: 0.8369 (ttt) REVERT: E 141 GLU cc_start: 0.8272 (mp0) cc_final: 0.7829 (mp0) REVERT: E 149 ARG cc_start: 0.8675 (ptt-90) cc_final: 0.6968 (ptm160) REVERT: E 168 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8189 (mt-10) REVERT: F 56 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8269 (p) REVERT: F 67 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.7911 (t0) REVERT: F 79 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.8111 (mtt-85) REVERT: F 96 ASP cc_start: 0.8515 (t70) cc_final: 0.8013 (t0) REVERT: F 132 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7932 (mt-10) REVERT: G 16 LYS cc_start: 0.7998 (tptt) cc_final: 0.7583 (tppt) REVERT: G 108 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8271 (mm-40) REVERT: G 138 GLU cc_start: 0.8463 (tt0) cc_final: 0.7978 (tt0) outliers start: 18 outliers final: 13 residues processed: 198 average time/residue: 0.3600 time to fit residues: 87.7486 Evaluate side-chains 182 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 67 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.086513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.073524 restraints weight = 37304.797| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 1.78 r_work: 0.2504 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2381 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9534 Z= 0.173 Angle : 0.530 7.228 12943 Z= 0.262 Chirality : 0.045 0.177 1428 Planarity : 0.004 0.040 1603 Dihedral : 5.938 38.522 1363 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.36 % Allowed : 15.21 % Favored : 82.43 % 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: 0.60 (0.28), residues: 1127 helix: 0.15 (0.31), residues: 294 sheet: -0.86 (0.27), residues: 322 loop : 1.81 (0.34), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 75 TYR 0.011 0.001 TYR C 35 PHE 0.020 0.002 PHE F 154 TRP 0.008 0.001 TRP G 172 HIS 0.003 0.000 HIS G 80 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9534) covalent geometry : angle 0.53002 (12943) hydrogen bonds : bond 0.03252 ( 287) hydrogen bonds : angle 4.06680 ( 819) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.9141 (p0) cc_final: 0.8927 (p0) REVERT: A 130 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7863 (mp) REVERT: A 171 GLU cc_start: 0.8989 (tp30) cc_final: 0.8624 (mm-30) REVERT: B 108 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8062 (mm110) REVERT: B 113 GLU cc_start: 0.8680 (mm-30) cc_final: 0.7801 (mm-30) REVERT: B 149 ARG cc_start: 0.9236 (ptt90) cc_final: 0.8774 (ptt-90) REVERT: C 67 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8357 (t0) REVERT: C 83 ARG cc_start: 0.8412 (ttp80) cc_final: 0.7984 (ttp80) REVERT: C 97 ARG cc_start: 0.8283 (ttm110) cc_final: 0.7920 (ttm110) REVERT: C 107 MET cc_start: 0.9255 (ttp) cc_final: 0.8859 (ttp) REVERT: C 149 ARG cc_start: 0.8958 (ptt-90) cc_final: 0.7358 (ptm-80) REVERT: D 57 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8586 (mp10) REVERT: D 107 MET cc_start: 0.8953 (ttp) cc_final: 0.7982 (ttp) REVERT: D 129 ASP cc_start: 0.8914 (p0) cc_final: 0.8661 (p0) REVERT: D 149 ARG cc_start: 0.9042 (ptt-90) cc_final: 0.7250 (ptm-80) REVERT: E 16 LYS cc_start: 0.7361 (tptm) cc_final: 0.6983 (tptm) REVERT: E 18 MET cc_start: 0.8765 (ttt) cc_final: 0.8390 (ttt) REVERT: E 141 GLU cc_start: 0.8269 (mp0) cc_final: 0.7925 (mp0) REVERT: E 149 ARG cc_start: 0.8632 (ptt-90) cc_final: 0.6891 (ptm160) REVERT: E 168 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8025 (mt-10) REVERT: F 56 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8278 (p) REVERT: F 67 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8285 (t0) REVERT: F 79 ARG cc_start: 0.8346 (mtt-85) cc_final: 0.8142 (mtt-85) REVERT: F 96 ASP cc_start: 0.8455 (t70) cc_final: 0.7865 (t0) REVERT: F 112 ASN cc_start: 0.8214 (m-40) cc_final: 0.7784 (m110) REVERT: F 132 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7891 (mt-10) REVERT: G 16 LYS cc_start: 0.8028 (tptt) cc_final: 0.7635 (tppt) REVERT: G 108 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8370 (mm-40) REVERT: G 149 ARG cc_start: 0.8985 (ptt90) cc_final: 0.8583 (ptt90) outliers start: 23 outliers final: 17 residues processed: 194 average time/residue: 0.3992 time to fit residues: 94.5754 Evaluate side-chains 189 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 85 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 46 optimal weight: 0.0040 chunk 73 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.086933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.073869 restraints weight = 37092.766| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 1.82 r_work: 0.2537 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9534 Z= 0.128 Angle : 0.496 7.059 12943 Z= 0.244 Chirality : 0.044 0.172 1428 Planarity : 0.003 0.039 1603 Dihedral : 5.630 35.218 1363 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.26 % Allowed : 15.31 % Favored : 82.43 % 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: 0.76 (0.27), residues: 1127 helix: 0.46 (0.32), residues: 294 sheet: -0.72 (0.27), residues: 322 loop : 1.75 (0.33), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 117 TYR 0.012 0.001 TYR C 35 PHE 0.014 0.001 PHE F 154 TRP 0.007 0.001 TRP G 66 HIS 0.002 0.000 HIS G 80 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9534) covalent geometry : angle 0.49615 (12943) hydrogen bonds : bond 0.02982 ( 287) hydrogen bonds : angle 3.87566 ( 819) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7857 (mp) REVERT: A 171 GLU cc_start: 0.8990 (tp30) cc_final: 0.8655 (mm-30) REVERT: B 113 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8218 (mm-30) REVERT: C 83 ARG cc_start: 0.8431 (ttp80) cc_final: 0.7995 (ttp80) REVERT: C 97 ARG cc_start: 0.8326 (ttm110) cc_final: 0.7984 (ttm110) REVERT: C 107 MET cc_start: 0.9233 (ttp) cc_final: 0.8891 (ttp) REVERT: C 149 ARG cc_start: 0.8918 (ptt-90) cc_final: 0.7291 (ptm-80) REVERT: D 107 MET cc_start: 0.8961 (ttp) cc_final: 0.8008 (ttp) REVERT: D 149 ARG cc_start: 0.9003 (ptt-90) cc_final: 0.7212 (ptm-80) REVERT: E 16 LYS cc_start: 0.7341 (tptm) cc_final: 0.6948 (tptm) REVERT: E 141 GLU cc_start: 0.8281 (mp0) cc_final: 0.7963 (mp0) REVERT: E 149 ARG cc_start: 0.8630 (ptt-90) cc_final: 0.6897 (ptm160) REVERT: E 168 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8101 (mt-10) REVERT: F 67 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.7861 (t0) REVERT: F 96 ASP cc_start: 0.8542 (t70) cc_final: 0.8005 (t0) REVERT: F 112 ASN cc_start: 0.8264 (m-40) cc_final: 0.7785 (m110) REVERT: F 132 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7956 (mt-10) REVERT: G 16 LYS cc_start: 0.8036 (tptt) cc_final: 0.7642 (tppt) REVERT: G 108 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8397 (mm-40) REVERT: G 149 ARG cc_start: 0.8944 (ptt90) cc_final: 0.8538 (ptt90) outliers start: 22 outliers final: 17 residues processed: 190 average time/residue: 0.3795 time to fit residues: 88.8536 Evaluate side-chains 187 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 45 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 75 optimal weight: 0.2980 chunk 98 optimal weight: 0.0070 chunk 103 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.087332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.074172 restraints weight = 36919.363| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 1.82 r_work: 0.2539 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2415 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9534 Z= 0.121 Angle : 0.492 6.987 12943 Z= 0.242 Chirality : 0.044 0.177 1428 Planarity : 0.003 0.037 1603 Dihedral : 5.423 33.975 1359 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.26 % Allowed : 15.52 % Favored : 82.22 % 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: 0.88 (0.28), residues: 1127 helix: 0.63 (0.33), residues: 294 sheet: -0.65 (0.27), residues: 322 loop : 1.77 (0.33), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 117 TYR 0.011 0.001 TYR D 35 PHE 0.013 0.001 PHE F 154 TRP 0.006 0.001 TRP E 66 HIS 0.002 0.000 HIS G 80 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9534) covalent geometry : angle 0.49240 (12943) hydrogen bonds : bond 0.02920 ( 287) hydrogen bonds : angle 3.81024 ( 819) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.8988 (tp30) cc_final: 0.8657 (mm-30) REVERT: B 108 GLN cc_start: 0.8115 (mm110) cc_final: 0.7433 (mm-40) REVERT: B 113 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8230 (mm-30) REVERT: C 56 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8313 (p) REVERT: C 67 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8407 (t0) REVERT: C 83 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8008 (ttp80) REVERT: C 97 ARG cc_start: 0.8332 (ttm110) cc_final: 0.7877 (ttm170) REVERT: C 107 MET cc_start: 0.9230 (ttp) cc_final: 0.8900 (ttp) REVERT: C 149 ARG cc_start: 0.8896 (ptt-90) cc_final: 0.7235 (ptm-80) REVERT: D 107 MET cc_start: 0.8944 (ttp) cc_final: 0.7997 (ttp) REVERT: D 149 ARG cc_start: 0.9013 (ptt-90) cc_final: 0.7223 (ptm-80) REVERT: D 155 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8956 (tt) REVERT: E 16 LYS cc_start: 0.7367 (tptm) cc_final: 0.6975 (tptm) REVERT: E 141 GLU cc_start: 0.8249 (mp0) cc_final: 0.7905 (mp0) REVERT: E 149 ARG cc_start: 0.8622 (ptt-90) cc_final: 0.6878 (ptm160) REVERT: E 168 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8093 (mt-10) REVERT: F 67 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.7852 (t0) REVERT: F 96 ASP cc_start: 0.8527 (t70) cc_final: 0.7996 (t0) REVERT: F 112 ASN cc_start: 0.8253 (m-40) cc_final: 0.7785 (m110) REVERT: F 132 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7947 (mt-10) REVERT: G 16 LYS cc_start: 0.8025 (tptt) cc_final: 0.7626 (tppt) REVERT: G 108 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8395 (mm-40) REVERT: G 149 ARG cc_start: 0.8954 (ptt90) cc_final: 0.8544 (ptt90) outliers start: 22 outliers final: 15 residues processed: 187 average time/residue: 0.3678 time to fit residues: 85.2318 Evaluate side-chains 185 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 62 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.089116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.075442 restraints weight = 37262.448| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 1.92 r_work: 0.2508 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2384 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 9534 Z= 0.203 Angle : 0.550 7.628 12943 Z= 0.271 Chirality : 0.046 0.180 1428 Planarity : 0.004 0.042 1603 Dihedral : 5.773 38.010 1359 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.88 % Allowed : 15.42 % Favored : 81.71 % 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: 0.63 (0.27), residues: 1127 helix: 0.49 (0.33), residues: 294 sheet: -0.55 (0.27), residues: 301 loop : 1.28 (0.31), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 117 TYR 0.013 0.002 TYR F 35 PHE 0.024 0.002 PHE F 154 TRP 0.009 0.001 TRP G 153 HIS 0.003 0.001 HIS G 80 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 9534) covalent geometry : angle 0.54971 (12943) hydrogen bonds : bond 0.03355 ( 287) hydrogen bonds : angle 4.02415 ( 819) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.9024 (tp30) cc_final: 0.8559 (mm-30) REVERT: B 108 GLN cc_start: 0.8128 (mm110) cc_final: 0.7806 (mm-40) REVERT: B 113 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8176 (mm-30) REVERT: C 56 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8250 (p) REVERT: C 67 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8491 (t0) REVERT: C 83 ARG cc_start: 0.8439 (ttp80) cc_final: 0.7973 (ttp80) REVERT: C 97 ARG cc_start: 0.8307 (ttm110) cc_final: 0.7867 (ttm170) REVERT: C 107 MET cc_start: 0.9261 (ttp) cc_final: 0.8914 (ttp) REVERT: C 149 ARG cc_start: 0.8897 (ptt-90) cc_final: 0.7246 (ptm-80) REVERT: D 107 MET cc_start: 0.8941 (ttp) cc_final: 0.7983 (ttp) REVERT: D 149 ARG cc_start: 0.9027 (ptt-90) cc_final: 0.7207 (ptm-80) REVERT: D 155 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8955 (tt) REVERT: D 171 GLU cc_start: 0.8849 (tp30) cc_final: 0.8347 (tt0) REVERT: E 16 LYS cc_start: 0.7430 (tptm) cc_final: 0.7043 (tptm) REVERT: E 141 GLU cc_start: 0.8271 (mp0) cc_final: 0.7944 (mp0) REVERT: E 149 ARG cc_start: 0.8666 (ptt-90) cc_final: 0.6885 (ptm160) REVERT: E 168 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8133 (mt-10) REVERT: F 67 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.7998 (t0) REVERT: F 96 ASP cc_start: 0.8524 (t70) cc_final: 0.8014 (t0) REVERT: F 112 ASN cc_start: 0.8256 (m-40) cc_final: 0.7818 (m110) REVERT: F 132 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7922 (mt-10) REVERT: G 16 LYS cc_start: 0.7964 (tptt) cc_final: 0.7553 (tppt) REVERT: G 108 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8356 (mm-40) REVERT: G 149 ARG cc_start: 0.8922 (ptt90) cc_final: 0.8506 (ptt90) outliers start: 28 outliers final: 23 residues processed: 189 average time/residue: 0.3690 time to fit residues: 86.6747 Evaluate side-chains 192 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.087147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.073643 restraints weight = 37109.335| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 1.87 r_work: 0.2528 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 9534 Z= 0.206 Angle : 0.549 7.742 12943 Z= 0.270 Chirality : 0.046 0.197 1428 Planarity : 0.004 0.051 1603 Dihedral : 5.762 39.343 1359 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.98 % Allowed : 15.31 % Favored : 81.71 % 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: 0.51 (0.27), residues: 1127 helix: 0.47 (0.32), residues: 294 sheet: -0.61 (0.27), residues: 301 loop : 1.14 (0.31), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 117 TYR 0.012 0.002 TYR F 35 PHE 0.020 0.002 PHE F 154 TRP 0.009 0.001 TRP G 172 HIS 0.003 0.000 HIS G 80 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 9534) covalent geometry : angle 0.54878 (12943) hydrogen bonds : bond 0.03336 ( 287) hydrogen bonds : angle 4.04795 ( 819) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.9035 (tp30) cc_final: 0.8580 (mm-30) REVERT: B 108 GLN cc_start: 0.8139 (mm110) cc_final: 0.7439 (mm-40) REVERT: C 56 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8288 (p) REVERT: C 67 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8551 (t0) REVERT: C 83 ARG cc_start: 0.8434 (ttp80) cc_final: 0.7990 (ttp80) REVERT: C 107 MET cc_start: 0.9283 (ttp) cc_final: 0.8915 (ttp) REVERT: C 149 ARG cc_start: 0.8930 (ptt-90) cc_final: 0.7274 (ptm-80) REVERT: D 107 MET cc_start: 0.8956 (ttp) cc_final: 0.7997 (ttp) REVERT: D 149 ARG cc_start: 0.9022 (ptt-90) cc_final: 0.7231 (ptm-80) REVERT: D 155 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8958 (tt) REVERT: D 171 GLU cc_start: 0.8854 (tp30) cc_final: 0.8358 (tt0) REVERT: E 16 LYS cc_start: 0.7474 (tptm) cc_final: 0.7089 (tptm) REVERT: E 93 ASP cc_start: 0.8326 (t0) cc_final: 0.8108 (t0) REVERT: E 141 GLU cc_start: 0.8276 (mp0) cc_final: 0.7932 (mp0) REVERT: E 149 ARG cc_start: 0.8629 (ptt-90) cc_final: 0.6781 (ptm160) REVERT: E 168 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8138 (mt-10) REVERT: F 67 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8398 (t0) REVERT: F 96 ASP cc_start: 0.8548 (t70) cc_final: 0.8037 (t0) REVERT: F 112 ASN cc_start: 0.8270 (m-40) cc_final: 0.7905 (m110) REVERT: F 132 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7945 (mt-10) REVERT: G 16 LYS cc_start: 0.7995 (tptt) cc_final: 0.7594 (tppt) REVERT: G 82 TYR cc_start: 0.9152 (m-10) cc_final: 0.8837 (m-10) REVERT: G 108 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8364 (mm-40) REVERT: G 149 ARG cc_start: 0.8907 (ptt90) cc_final: 0.8522 (ptt90) outliers start: 29 outliers final: 24 residues processed: 194 average time/residue: 0.3775 time to fit residues: 90.5118 Evaluate side-chains 195 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.088054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.074506 restraints weight = 36887.990| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 1.88 r_work: 0.2544 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9534 Z= 0.135 Angle : 0.502 7.047 12943 Z= 0.247 Chirality : 0.044 0.195 1428 Planarity : 0.003 0.039 1603 Dihedral : 5.511 37.396 1359 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.47 % Allowed : 15.72 % Favored : 81.81 % 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: 0.62 (0.27), residues: 1127 helix: 0.60 (0.33), residues: 294 sheet: -0.78 (0.27), residues: 322 loop : 1.44 (0.32), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 117 TYR 0.011 0.001 TYR D 35 PHE 0.013 0.001 PHE F 154 TRP 0.007 0.001 TRP G 66 HIS 0.002 0.000 HIS G 80 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9534) covalent geometry : angle 0.50189 (12943) hydrogen bonds : bond 0.02982 ( 287) hydrogen bonds : angle 3.86622 ( 819) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.9023 (tp30) cc_final: 0.8654 (mm-30) REVERT: B 108 GLN cc_start: 0.8123 (mm110) cc_final: 0.7724 (mm-40) REVERT: C 56 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8274 (p) REVERT: C 67 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8455 (t0) REVERT: C 83 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8004 (ttp80) REVERT: C 107 MET cc_start: 0.9252 (ttp) cc_final: 0.8915 (ttp) REVERT: C 149 ARG cc_start: 0.8895 (ptt-90) cc_final: 0.7233 (ptm-80) REVERT: D 79 ARG cc_start: 0.8544 (mtt90) cc_final: 0.8155 (mtp85) REVERT: D 107 MET cc_start: 0.8952 (ttp) cc_final: 0.7976 (ttp) REVERT: D 149 ARG cc_start: 0.9017 (ptt-90) cc_final: 0.7221 (ptm-80) REVERT: D 155 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8953 (tt) REVERT: D 171 GLU cc_start: 0.8826 (tp30) cc_final: 0.8244 (tt0) REVERT: E 141 GLU cc_start: 0.8272 (mp0) cc_final: 0.7942 (mp0) REVERT: E 149 ARG cc_start: 0.8631 (ptt-90) cc_final: 0.6716 (ptm160) REVERT: E 168 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8108 (mt-10) REVERT: F 67 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.7957 (t0) REVERT: F 96 ASP cc_start: 0.8532 (t70) cc_final: 0.8016 (t0) REVERT: F 112 ASN cc_start: 0.8264 (m-40) cc_final: 0.7912 (m110) REVERT: F 132 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7931 (mt-10) REVERT: G 16 LYS cc_start: 0.7990 (tptt) cc_final: 0.7590 (tppt) REVERT: G 108 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8355 (mm-40) REVERT: G 149 ARG cc_start: 0.8866 (ptt90) cc_final: 0.8490 (ptt90) outliers start: 24 outliers final: 20 residues processed: 188 average time/residue: 0.3718 time to fit residues: 86.2033 Evaluate side-chains 191 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.086822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.073474 restraints weight = 37360.201| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 1.87 r_work: 0.2541 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2417 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9534 Z= 0.161 Angle : 0.520 7.264 12943 Z= 0.256 Chirality : 0.045 0.209 1428 Planarity : 0.004 0.046 1603 Dihedral : 5.571 37.667 1359 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.57 % Allowed : 15.83 % Favored : 81.60 % 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: 0.60 (0.27), residues: 1127 helix: 0.57 (0.33), residues: 294 sheet: -0.55 (0.28), residues: 301 loop : 1.18 (0.31), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 117 TYR 0.012 0.001 TYR D 35 PHE 0.017 0.002 PHE F 154 TRP 0.008 0.001 TRP G 153 HIS 0.002 0.000 HIS G 80 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9534) covalent geometry : angle 0.52040 (12943) hydrogen bonds : bond 0.03088 ( 287) hydrogen bonds : angle 3.90042 ( 819) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.9018 (tp30) cc_final: 0.8646 (mm-30) REVERT: B 108 GLN cc_start: 0.8123 (mm110) cc_final: 0.7803 (mm-40) REVERT: C 56 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8286 (p) REVERT: C 67 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8504 (t0) REVERT: C 83 ARG cc_start: 0.8425 (ttp80) cc_final: 0.7991 (ttp80) REVERT: C 107 MET cc_start: 0.9256 (ttp) cc_final: 0.8915 (ttp) REVERT: C 149 ARG cc_start: 0.8895 (ptt-90) cc_final: 0.7235 (ptm-80) REVERT: D 79 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8165 (mtp85) REVERT: D 107 MET cc_start: 0.8924 (ttp) cc_final: 0.7954 (ttp) REVERT: D 149 ARG cc_start: 0.9012 (ptt-90) cc_final: 0.7227 (ptm-80) REVERT: D 155 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8955 (tt) REVERT: D 171 GLU cc_start: 0.8830 (tp30) cc_final: 0.8253 (tt0) REVERT: E 16 LYS cc_start: 0.7654 (tptp) cc_final: 0.7272 (tptp) REVERT: E 141 GLU cc_start: 0.8263 (mp0) cc_final: 0.7936 (mp0) REVERT: E 149 ARG cc_start: 0.8633 (ptt-90) cc_final: 0.6724 (ptm160) REVERT: E 168 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8109 (mt-10) REVERT: F 67 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.7963 (t0) REVERT: F 96 ASP cc_start: 0.8532 (t70) cc_final: 0.8024 (t0) REVERT: F 112 ASN cc_start: 0.8267 (m-40) cc_final: 0.7866 (m110) REVERT: F 132 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7937 (mt-10) REVERT: G 16 LYS cc_start: 0.7994 (tptt) cc_final: 0.7592 (tppt) REVERT: G 108 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8357 (mm-40) REVERT: G 149 ARG cc_start: 0.8877 (ptt90) cc_final: 0.8501 (ptt90) outliers start: 25 outliers final: 20 residues processed: 187 average time/residue: 0.3529 time to fit residues: 81.9114 Evaluate side-chains 192 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.087886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.074486 restraints weight = 37063.782| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 1.86 r_work: 0.2535 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2411 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9534 Z= 0.133 Angle : 0.503 7.123 12943 Z= 0.247 Chirality : 0.044 0.215 1428 Planarity : 0.003 0.044 1603 Dihedral : 5.475 36.750 1359 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.57 % Allowed : 16.03 % Favored : 81.40 % 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: 0.69 (0.27), residues: 1127 helix: 0.65 (0.33), residues: 294 sheet: -0.52 (0.28), residues: 301 loop : 1.25 (0.31), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 117 TYR 0.011 0.001 TYR D 35 PHE 0.012 0.001 PHE F 154 TRP 0.007 0.001 TRP G 66 HIS 0.001 0.000 HIS G 80 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9534) covalent geometry : angle 0.50338 (12943) hydrogen bonds : bond 0.02965 ( 287) hydrogen bonds : angle 3.82925 ( 819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4879.23 seconds wall clock time: 83 minutes 16.46 seconds (4996.46 seconds total)