Starting phenix.real_space_refine on Mon Jun 16 08:46:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s5e_19733/06_2025/8s5e_19733_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s5e_19733/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8s5e_19733/06_2025/8s5e_19733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s5e_19733/06_2025/8s5e_19733.map" model { file = "/net/cci-nas-00/data/ceres_data/8s5e_19733/06_2025/8s5e_19733_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s5e_19733/06_2025/8s5e_19733_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.308 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.07, per 1000 atoms: 0.54 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: 4.88 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.43 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: 6.85 Time building geometry restraints manager: 5.95 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.340 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 42.190 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.700 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (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 TRP 0.009 0.002 TRP F 153 HIS 0.002 0.001 HIS E 80 PHE 0.011 0.002 PHE F 154 TYR 0.007 0.001 TYR B 35 ARG 0.004 0.001 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.15444 ( 287) hydrogen bonds : angle 6.09332 ( 819) covalent geometry : bond 0.01678 ( 9534) covalent geometry : angle 0.99079 (12943) *********************** 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 : 1.386 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: 0.7859 (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: 0.7466 (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: 0.6088 time to fit residues: 229.8939 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 : 1.349 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 57 optimal weight: 0.4980 chunk 45 optimal weight: 0.3980 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN C 118 ASN E 108 GLN E 156 GLN G 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.089184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.076128 restraints weight = 36378.957| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 1.79 r_work: 0.2546 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2422 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2165 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= 0.129 Angle : 0.536 6.902 12943 Z= 0.264 Chirality : 0.044 0.182 1428 Planarity : 0.004 0.045 1603 Dihedral : 7.070 54.334 1385 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.95 % Allowed : 14.39 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.27), residues: 1127 helix: -1.09 (0.29), residues: 294 sheet: -1.14 (0.26), residues: 308 loop : 1.85 (0.34), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 66 HIS 0.002 0.000 HIS G 80 PHE 0.010 0.001 PHE F 154 TYR 0.012 0.001 TYR C 35 ARG 0.005 0.001 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 287) hydrogen bonds : angle 4.31769 ( 819) covalent geometry : bond 0.00281 ( 9534) covalent geometry : angle 0.53631 (12943) *********************** 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 207 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.9106 (tptp) cc_final: 0.8905 (tptm) REVERT: A 149 ARG cc_start: 0.9265 (ptt-90) cc_final: 0.8864 (ptt90) REVERT: A 171 GLU cc_start: 0.8757 (tp30) cc_final: 0.8505 (mm-30) REVERT: B 113 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7839 (mm-30) REVERT: B 118 ASN cc_start: 0.8917 (m-40) cc_final: 0.8658 (m-40) REVERT: B 149 ARG cc_start: 0.9177 (ptt-90) cc_final: 0.8958 (ptt90) REVERT: B 150 ASN cc_start: 0.8438 (p0) cc_final: 0.8112 (p0) REVERT: C 59 LYS cc_start: 0.7798 (mtpp) cc_final: 0.7557 (mtpt) REVERT: C 67 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8299 (t0) REVERT: C 71 GLN cc_start: 0.8616 (mt0) cc_final: 0.8376 (mt0) REVERT: C 83 ARG cc_start: 0.8283 (ttp80) cc_final: 0.7773 (ttp80) REVERT: C 97 ARG cc_start: 0.8349 (ttm110) cc_final: 0.7993 (ttm170) REVERT: C 107 MET cc_start: 0.9269 (ttp) cc_final: 0.8787 (ttp) REVERT: C 149 ARG cc_start: 0.9048 (ptt-90) cc_final: 0.7600 (ptm-80) REVERT: C 171 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8405 (mm-30) REVERT: D 18 MET cc_start: 0.8699 (ttt) cc_final: 0.8206 (ttt) REVERT: D 26 ASP cc_start: 0.9199 (p0) cc_final: 0.8990 (p0) REVERT: D 83 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7800 (ttm-80) REVERT: D 107 MET cc_start: 0.9117 (ttp) cc_final: 0.8246 (ttp) REVERT: D 110 MET cc_start: 0.8757 (ttp) cc_final: 0.8552 (ttm) REVERT: D 149 ARG cc_start: 0.9110 (ptt-90) cc_final: 0.7405 (ptm-80) REVERT: E 18 MET cc_start: 0.8610 (ttt) cc_final: 0.8212 (ttt) REVERT: E 110 MET cc_start: 0.9103 (ttp) cc_final: 0.8891 (ttm) REVERT: E 149 ARG cc_start: 0.8832 (ptt-90) cc_final: 0.7173 (ptm160) REVERT: E 168 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8133 (mt-10) REVERT: F 56 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8324 (p) REVERT: F 67 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.7817 (t0) REVERT: F 79 ARG cc_start: 0.8201 (mtt-85) cc_final: 0.7906 (mtt-85) REVERT: F 96 ASP cc_start: 0.8365 (t70) cc_final: 0.7951 (t0) REVERT: F 161 THR cc_start: 0.8142 (p) cc_final: 0.7911 (p) REVERT: G 16 LYS cc_start: 0.7921 (tptt) cc_final: 0.7573 (tppt) REVERT: G 107 MET cc_start: 0.8974 (ttp) cc_final: 0.8738 (ttp) REVERT: G 108 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8216 (mm-40) REVERT: G 126 ASN cc_start: 0.9000 (t0) cc_final: 0.8784 (t0) REVERT: G 138 GLU cc_start: 0.8272 (tt0) cc_final: 0.7936 (tt0) REVERT: G 142 LYS cc_start: 0.8496 (mttp) cc_final: 0.8278 (mttp) outliers start: 19 outliers final: 11 residues processed: 199 average time/residue: 0.7151 time to fit residues: 178.8551 Evaluate side-chains 186 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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 58 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- 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 = 0.2791 r_free = 0.2791 target = 0.085088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.072367 restraints weight = 37479.133| |-----------------------------------------------------------------------------| r_work (start): 0.2613 rms_B_bonded: 1.75 r_work: 0.2501 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2379 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 9534 Z= 0.218 Angle : 0.589 8.177 12943 Z= 0.289 Chirality : 0.046 0.171 1428 Planarity : 0.004 0.042 1603 Dihedral : 6.432 40.248 1367 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.06 % Allowed : 14.29 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.27), residues: 1127 helix: -0.31 (0.30), residues: 294 sheet: -0.93 (0.26), residues: 322 loop : 1.76 (0.34), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 66 HIS 0.005 0.001 HIS G 80 PHE 0.025 0.002 PHE F 154 TYR 0.013 0.002 TYR E 35 ARG 0.006 0.001 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 287) hydrogen bonds : angle 4.34546 ( 819) covalent geometry : bond 0.00509 ( 9534) covalent geometry : angle 0.58919 (12943) *********************** 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 199 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7769 (mp) REVERT: A 171 GLU cc_start: 0.8941 (tp30) cc_final: 0.8512 (mm-30) REVERT: B 79 ARG cc_start: 0.8432 (mtt-85) cc_final: 0.8082 (mtt180) REVERT: B 113 GLU cc_start: 0.8680 (mm-30) cc_final: 0.7904 (mm-30) REVERT: C 83 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8036 (ttp80) REVERT: C 97 ARG cc_start: 0.8375 (ttm110) cc_final: 0.8087 (ttm110) REVERT: C 107 MET cc_start: 0.9312 (ttp) cc_final: 0.8892 (ttp) REVERT: C 149 ARG cc_start: 0.8989 (ptt-90) cc_final: 0.7420 (ptm-80) REVERT: D 17 GLU cc_start: 0.8483 (tt0) cc_final: 0.7895 (tp30) REVERT: D 18 MET cc_start: 0.8807 (ttt) cc_final: 0.8237 (ttt) REVERT: D 83 ARG cc_start: 0.8514 (ttp80) cc_final: 0.8180 (ttm-80) REVERT: D 107 MET cc_start: 0.9041 (ttp) cc_final: 0.8028 (ttp) REVERT: D 129 ASP cc_start: 0.8847 (p0) cc_final: 0.8587 (p0) REVERT: D 149 ARG cc_start: 0.9062 (ptt-90) cc_final: 0.7314 (ptm-80) REVERT: E 18 MET cc_start: 0.8795 (ttt) cc_final: 0.8424 (ttt) REVERT: E 110 MET cc_start: 0.9239 (ttp) cc_final: 0.8997 (ttm) REVERT: E 141 GLU cc_start: 0.8371 (mp0) cc_final: 0.7928 (mp0) REVERT: E 149 ARG cc_start: 0.8669 (ptt-90) cc_final: 0.6937 (ptm160) REVERT: E 168 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8123 (mt-10) REVERT: F 56 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8334 (p) REVERT: F 67 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.7994 (t0) REVERT: F 79 ARG cc_start: 0.8333 (mtt-85) cc_final: 0.8122 (mtt-85) REVERT: F 96 ASP cc_start: 0.8564 (t70) cc_final: 0.8066 (t0) REVERT: F 132 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7900 (mt-10) REVERT: G 16 LYS cc_start: 0.8033 (tptt) cc_final: 0.7647 (tppt) REVERT: G 108 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8302 (mm-40) REVERT: G 138 GLU cc_start: 0.8510 (tt0) cc_final: 0.8041 (tt0) REVERT: G 149 ARG cc_start: 0.9132 (ptt-90) cc_final: 0.8766 (ptt90) REVERT: G 167 TYR cc_start: 0.9083 (m-80) cc_final: 0.8601 (m-10) outliers start: 20 outliers final: 15 residues processed: 195 average time/residue: 0.8059 time to fit residues: 195.7830 Evaluate side-chains 183 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 2.338 ------------------------------------------------------------------------------- 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 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 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 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 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 42 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN D 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.086494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.073619 restraints weight = 37356.387| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 1.76 r_work: 0.2500 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2378 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3380 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= 0.174 Angle : 0.529 7.220 12943 Z= 0.262 Chirality : 0.045 0.171 1428 Planarity : 0.004 0.040 1603 Dihedral : 6.037 39.151 1365 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.88 % Allowed : 14.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.27), residues: 1127 helix: 0.12 (0.31), residues: 294 sheet: -0.88 (0.27), residues: 322 loop : 1.68 (0.33), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 66 HIS 0.003 0.000 HIS G 80 PHE 0.020 0.002 PHE F 154 TYR 0.012 0.001 TYR C 35 ARG 0.003 0.000 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 287) hydrogen bonds : angle 4.10690 ( 819) covalent geometry : bond 0.00398 ( 9534) covalent geometry : angle 0.52894 (12943) *********************** 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 200 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7869 (mp) REVERT: A 171 GLU cc_start: 0.8992 (tp30) cc_final: 0.8623 (mm-30) REVERT: B 108 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8189 (mm110) REVERT: C 67 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8423 (t0) REVERT: C 83 ARG cc_start: 0.8397 (ttp80) cc_final: 0.7957 (ttp80) REVERT: C 97 ARG cc_start: 0.8272 (ttm110) cc_final: 0.7900 (ttm110) REVERT: C 107 MET cc_start: 0.9240 (ttp) cc_final: 0.8844 (ttp) REVERT: C 149 ARG cc_start: 0.8941 (ptt-90) cc_final: 0.7346 (ptm-80) REVERT: D 57 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8576 (mp10) REVERT: D 79 ARG cc_start: 0.8552 (mtt90) cc_final: 0.8194 (mtp85) REVERT: D 107 MET cc_start: 0.8942 (ttp) cc_final: 0.7964 (ttp) REVERT: D 129 ASP cc_start: 0.8921 (p0) cc_final: 0.8665 (p0) REVERT: D 149 ARG cc_start: 0.9045 (ptt-90) cc_final: 0.7232 (ptm-80) REVERT: E 16 LYS cc_start: 0.7605 (tptp) cc_final: 0.7193 (tptm) REVERT: E 110 MET cc_start: 0.9224 (ttp) cc_final: 0.8977 (ttm) REVERT: E 141 GLU cc_start: 0.8245 (mp0) cc_final: 0.7921 (mp0) REVERT: E 149 ARG cc_start: 0.8620 (ptt-90) cc_final: 0.6884 (ptm160) REVERT: E 168 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8060 (mt-10) REVERT: F 56 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8264 (p) REVERT: F 67 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8236 (t0) REVERT: F 79 ARG cc_start: 0.8332 (mtt-85) cc_final: 0.8128 (mtt-85) REVERT: F 96 ASP cc_start: 0.8414 (t70) cc_final: 0.7848 (t0) REVERT: F 112 ASN cc_start: 0.8203 (m-40) cc_final: 0.7778 (m110) REVERT: F 132 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7913 (mt-10) REVERT: G 16 LYS cc_start: 0.8001 (tptt) cc_final: 0.7601 (tppt) REVERT: G 108 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8362 (mm-40) REVERT: G 138 GLU cc_start: 0.8428 (tt0) cc_final: 0.8048 (tt0) REVERT: G 149 ARG cc_start: 0.9112 (ptt-90) cc_final: 0.8822 (ptt90) REVERT: G 167 TYR cc_start: 0.9009 (m-80) cc_final: 0.8675 (m-80) outliers start: 28 outliers final: 21 residues processed: 196 average time/residue: 0.7463 time to fit residues: 182.3446 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 : 1.539 ------------------------------------------------------------------------------- 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 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 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 91 VAL Chi-restraints excluded: chain D residue 134 MET 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 56 VAL Chi-restraints excluded: chain F residue 67 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 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 82 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.2805 r_free = 0.2805 target = 0.086112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.072987 restraints weight = 37653.006| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 1.82 r_work: 0.2497 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2374 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3550 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= 0.165 Angle : 0.526 7.437 12943 Z= 0.259 Chirality : 0.045 0.169 1428 Planarity : 0.004 0.039 1603 Dihedral : 5.948 38.965 1365 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.77 % Allowed : 15.11 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.27), residues: 1127 helix: 0.35 (0.32), residues: 294 sheet: -0.81 (0.27), residues: 322 loop : 1.52 (0.32), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 66 HIS 0.002 0.000 HIS G 80 PHE 0.019 0.002 PHE F 154 TYR 0.012 0.001 TYR C 35 ARG 0.004 0.000 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 287) hydrogen bonds : angle 4.02099 ( 819) covalent geometry : bond 0.00381 ( 9534) covalent geometry : angle 0.52584 (12943) *********************** 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 197 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7866 (mp) REVERT: A 171 GLU cc_start: 0.8947 (tp30) cc_final: 0.8575 (mm-30) REVERT: C 67 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8431 (t0) REVERT: C 83 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8000 (ttp80) REVERT: C 97 ARG cc_start: 0.8329 (ttm110) cc_final: 0.7913 (ttm170) REVERT: C 107 MET cc_start: 0.9233 (ttp) cc_final: 0.8881 (ttp) REVERT: C 149 ARG cc_start: 0.8947 (ptt-90) cc_final: 0.7341 (ptm-80) REVERT: D 79 ARG cc_start: 0.8613 (mtt90) cc_final: 0.8216 (mtp85) REVERT: D 107 MET cc_start: 0.8958 (ttp) cc_final: 0.7999 (ttp) REVERT: D 149 ARG cc_start: 0.9028 (ptt-90) cc_final: 0.7212 (ptm-80) REVERT: D 155 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8959 (tt) REVERT: D 171 GLU cc_start: 0.8852 (tp30) cc_final: 0.8388 (tt0) REVERT: E 16 LYS cc_start: 0.7618 (tptp) cc_final: 0.7176 (tptm) REVERT: E 141 GLU cc_start: 0.8257 (mp0) cc_final: 0.7932 (mp0) REVERT: E 149 ARG cc_start: 0.8618 (ptt-90) cc_final: 0.6866 (ptm160) REVERT: E 168 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8137 (mt-10) REVERT: F 67 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8341 (t0) REVERT: F 96 ASP cc_start: 0.8531 (t70) cc_final: 0.7975 (t0) REVERT: F 112 ASN cc_start: 0.8247 (m-40) cc_final: 0.7778 (m110) REVERT: F 132 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7889 (mt-10) REVERT: G 16 LYS cc_start: 0.8007 (tptt) cc_final: 0.7609 (tppt) REVERT: G 108 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8384 (mm-40) REVERT: G 138 GLU cc_start: 0.8423 (tt0) cc_final: 0.8038 (tt0) REVERT: G 149 ARG cc_start: 0.9124 (ptt-90) cc_final: 0.8836 (ptt90) outliers start: 27 outliers final: 19 residues processed: 191 average time/residue: 0.7763 time to fit residues: 184.9261 Evaluate side-chains 190 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 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 91 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 103 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.2817 r_free = 0.2817 target = 0.086765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.073692 restraints weight = 37472.064| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 1.80 r_work: 0.2505 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2383 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9534 Z= 0.149 Angle : 0.511 7.201 12943 Z= 0.252 Chirality : 0.044 0.177 1428 Planarity : 0.003 0.038 1603 Dihedral : 5.760 38.054 1363 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.19 % Allowed : 14.70 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.27), residues: 1127 helix: 0.46 (0.32), residues: 294 sheet: -0.81 (0.27), residues: 322 loop : 1.52 (0.32), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 66 HIS 0.001 0.000 HIS G 80 PHE 0.016 0.001 PHE F 154 TYR 0.012 0.001 TYR E 35 ARG 0.006 0.000 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.03104 ( 287) hydrogen bonds : angle 3.94140 ( 819) covalent geometry : bond 0.00343 ( 9534) covalent geometry : angle 0.51064 (12943) *********************** 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 200 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 2.199 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7834 (mp) REVERT: A 171 GLU cc_start: 0.8941 (tp30) cc_final: 0.8570 (mm-30) REVERT: B 108 GLN cc_start: 0.8075 (mm110) cc_final: 0.7643 (mm-40) REVERT: C 67 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8500 (t0) REVERT: C 83 ARG cc_start: 0.8430 (ttp80) cc_final: 0.7970 (ttp80) REVERT: C 107 MET cc_start: 0.9214 (ttp) cc_final: 0.8863 (ttp) REVERT: C 149 ARG cc_start: 0.8926 (ptt-90) cc_final: 0.7258 (ptm-80) REVERT: D 57 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8581 (mp10) REVERT: D 79 ARG cc_start: 0.8599 (mtt90) cc_final: 0.8198 (mtp85) REVERT: D 107 MET cc_start: 0.8915 (ttp) cc_final: 0.7946 (ttp) REVERT: D 149 ARG cc_start: 0.9028 (ptt-90) cc_final: 0.7201 (ptm-80) REVERT: D 155 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8955 (tt) REVERT: D 171 GLU cc_start: 0.8817 (tp30) cc_final: 0.8234 (tt0) REVERT: E 16 LYS cc_start: 0.7606 (tptp) cc_final: 0.7153 (tptm) REVERT: E 141 GLU cc_start: 0.8251 (mp0) cc_final: 0.7927 (mp0) REVERT: E 149 ARG cc_start: 0.8581 (ptt-90) cc_final: 0.6721 (ptm160) REVERT: E 168 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8108 (mt-10) REVERT: F 67 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8371 (t0) REVERT: F 96 ASP cc_start: 0.8490 (t70) cc_final: 0.7943 (t0) REVERT: F 112 ASN cc_start: 0.8212 (m-40) cc_final: 0.7764 (m110) REVERT: F 132 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7861 (mt-10) REVERT: G 16 LYS cc_start: 0.7985 (tptt) cc_final: 0.7578 (tppt) REVERT: G 82 TYR cc_start: 0.9174 (m-10) cc_final: 0.8782 (m-10) REVERT: G 108 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8355 (mm-40) REVERT: G 138 GLU cc_start: 0.8415 (tt0) cc_final: 0.8045 (tt0) REVERT: G 149 ARG cc_start: 0.9136 (ptt-90) cc_final: 0.8833 (ptt90) outliers start: 31 outliers final: 23 residues processed: 194 average time/residue: 0.8681 time to fit residues: 216.1371 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 : 2.215 ------------------------------------------------------------------------------- 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 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 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 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 176 SER Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 85 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.2812 r_free = 0.2812 target = 0.086430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.073377 restraints weight = 37174.781| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 1.80 r_work: 0.2503 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2380 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9534 Z= 0.168 Angle : 0.524 7.362 12943 Z= 0.258 Chirality : 0.045 0.185 1428 Planarity : 0.004 0.042 1603 Dihedral : 5.821 38.678 1363 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.27), residues: 1127 helix: 0.48 (0.32), residues: 294 sheet: -0.83 (0.26), residues: 322 loop : 1.42 (0.32), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 172 HIS 0.002 0.000 HIS G 80 PHE 0.016 0.002 PHE E 154 TYR 0.012 0.001 TYR D 35 ARG 0.006 0.000 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 287) hydrogen bonds : angle 3.96627 ( 819) covalent geometry : bond 0.00388 ( 9534) covalent geometry : angle 0.52446 (12943) *********************** 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 193 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 3.316 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7854 (mp) REVERT: A 171 GLU cc_start: 0.8945 (tp30) cc_final: 0.8562 (mm-30) REVERT: B 108 GLN cc_start: 0.8154 (mm110) cc_final: 0.7866 (mm-40) REVERT: C 67 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8509 (t0) REVERT: C 83 ARG cc_start: 0.8450 (ttp80) cc_final: 0.7987 (ttp80) REVERT: C 107 MET cc_start: 0.9230 (ttp) cc_final: 0.8855 (ttp) REVERT: C 149 ARG cc_start: 0.8928 (ptt-90) cc_final: 0.7269 (ptm-80) REVERT: D 79 ARG cc_start: 0.8632 (mtt90) cc_final: 0.8236 (mtp85) REVERT: D 107 MET cc_start: 0.8936 (ttp) cc_final: 0.7977 (ttp) REVERT: D 149 ARG cc_start: 0.9026 (ptt-90) cc_final: 0.7215 (ptm-80) REVERT: D 155 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8939 (tt) REVERT: D 171 GLU cc_start: 0.8828 (tp30) cc_final: 0.8252 (tt0) REVERT: E 141 GLU cc_start: 0.8259 (mp0) cc_final: 0.7930 (mp0) REVERT: E 149 ARG cc_start: 0.8635 (ptt-90) cc_final: 0.6734 (ptm160) REVERT: E 168 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8112 (mt-10) REVERT: F 67 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8399 (t0) REVERT: F 96 ASP cc_start: 0.8531 (t70) cc_final: 0.8007 (t0) REVERT: F 112 ASN cc_start: 0.8234 (m-40) cc_final: 0.7792 (m110) REVERT: F 132 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7872 (mt-10) REVERT: G 16 LYS cc_start: 0.7996 (tptt) cc_final: 0.7591 (tppt) REVERT: G 108 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8367 (mm-40) REVERT: G 138 GLU cc_start: 0.8345 (tt0) cc_final: 0.7969 (tt0) REVERT: G 149 ARG cc_start: 0.9122 (ptt-90) cc_final: 0.8830 (ptt90) outliers start: 28 outliers final: 22 residues processed: 190 average time/residue: 0.9766 time to fit residues: 242.6441 Evaluate side-chains 189 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 2.744 ------------------------------------------------------------------------------- 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 85 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 45 THR 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 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 E residue 62 SER 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 176 SER Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 67 ASP 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 59 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.086731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.073593 restraints weight = 37188.090| |-----------------------------------------------------------------------------| r_work (start): 0.2619 rms_B_bonded: 1.82 r_work: 0.2506 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2384 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9534 Z= 0.132 Angle : 0.498 7.054 12943 Z= 0.245 Chirality : 0.044 0.186 1428 Planarity : 0.003 0.039 1603 Dihedral : 5.568 36.875 1361 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.36 % Allowed : 15.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.27), residues: 1127 helix: 0.60 (0.33), residues: 294 sheet: -0.77 (0.27), residues: 322 loop : 1.49 (0.32), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 66 HIS 0.001 0.000 HIS G 80 PHE 0.012 0.001 PHE F 154 TYR 0.012 0.001 TYR C 35 ARG 0.007 0.000 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 287) hydrogen bonds : angle 3.84801 ( 819) covalent geometry : bond 0.00302 ( 9534) covalent geometry : angle 0.49765 (12943) *********************** 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 192 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7851 (mp) REVERT: A 171 GLU cc_start: 0.8957 (tp30) cc_final: 0.8589 (mm-30) REVERT: B 108 GLN cc_start: 0.8181 (mm110) cc_final: 0.7788 (mm-40) REVERT: C 67 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8425 (t0) REVERT: C 83 ARG cc_start: 0.8431 (ttp80) cc_final: 0.7994 (ttp80) REVERT: C 107 MET cc_start: 0.9217 (ttp) cc_final: 0.8872 (ttp) REVERT: C 149 ARG cc_start: 0.8919 (ptt-90) cc_final: 0.7255 (ptm-80) REVERT: D 57 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8326 (mp10) REVERT: D 79 ARG cc_start: 0.8634 (mtt90) cc_final: 0.8237 (mtp85) REVERT: D 107 MET cc_start: 0.8955 (ttp) cc_final: 0.8255 (ttp) REVERT: D 149 ARG cc_start: 0.9020 (ptt-90) cc_final: 0.7221 (ptm-80) REVERT: D 155 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8930 (tt) REVERT: D 171 GLU cc_start: 0.8819 (tp30) cc_final: 0.8238 (tt0) REVERT: E 16 LYS cc_start: 0.7635 (tptp) cc_final: 0.7276 (tptp) REVERT: E 141 GLU cc_start: 0.8270 (mp0) cc_final: 0.7962 (mp0) REVERT: E 149 ARG cc_start: 0.8666 (ptt-90) cc_final: 0.6723 (ptm160) REVERT: E 168 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8097 (mt-10) REVERT: F 67 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.7954 (t0) REVERT: F 96 ASP cc_start: 0.8442 (t70) cc_final: 0.7901 (t0) REVERT: F 112 ASN cc_start: 0.8237 (m-40) cc_final: 0.7802 (m110) REVERT: F 132 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7858 (mt-10) REVERT: G 16 LYS cc_start: 0.8005 (tptt) cc_final: 0.7602 (tppt) REVERT: G 82 TYR cc_start: 0.9146 (m-10) cc_final: 0.8910 (m-10) REVERT: G 108 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8360 (mm-40) REVERT: G 138 GLU cc_start: 0.8344 (tt0) cc_final: 0.7991 (tt0) REVERT: G 149 ARG cc_start: 0.9094 (ptt-90) cc_final: 0.8813 (ptt90) outliers start: 23 outliers final: 16 residues processed: 188 average time/residue: 0.7369 time to fit residues: 173.4363 Evaluate side-chains 186 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 56 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 110 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.2833 r_free = 0.2833 target = 0.086949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.073508 restraints weight = 37425.510| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 1.87 r_work: 0.2534 rms_B_bonded: 2.11 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: 0.8476 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9534 Z= 0.171 Angle : 0.525 7.297 12943 Z= 0.259 Chirality : 0.045 0.196 1428 Planarity : 0.004 0.044 1603 Dihedral : 5.642 37.909 1359 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.67 % Allowed : 15.42 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.27), residues: 1127 helix: 0.55 (0.33), residues: 294 sheet: -0.83 (0.27), residues: 322 loop : 1.39 (0.32), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 153 HIS 0.002 0.000 HIS G 80 PHE 0.017 0.002 PHE E 154 TYR 0.013 0.001 TYR D 35 ARG 0.007 0.000 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 287) hydrogen bonds : angle 3.92145 ( 819) covalent geometry : bond 0.00396 ( 9534) covalent geometry : angle 0.52503 (12943) *********************** 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 195 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 1.480 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7738 (mp) REVERT: A 171 GLU cc_start: 0.9042 (tp30) cc_final: 0.8595 (mm-30) REVERT: B 108 GLN cc_start: 0.8116 (mm110) cc_final: 0.7797 (mm-40) REVERT: C 67 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8511 (t0) REVERT: C 83 ARG cc_start: 0.8396 (ttp80) cc_final: 0.7951 (ttp80) REVERT: C 107 MET cc_start: 0.9264 (ttp) cc_final: 0.8917 (ttp) REVERT: C 149 ARG cc_start: 0.8881 (ptt-90) cc_final: 0.7251 (ptm-80) REVERT: D 79 ARG cc_start: 0.8665 (mtt90) cc_final: 0.8275 (mtp85) REVERT: D 107 MET cc_start: 0.8937 (ttp) cc_final: 0.7966 (ttp) REVERT: D 149 ARG cc_start: 0.9015 (ptt-90) cc_final: 0.7231 (ptm-80) REVERT: D 155 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8936 (tt) REVERT: D 171 GLU cc_start: 0.8830 (tp30) cc_final: 0.8262 (tt0) REVERT: E 110 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8966 (ttm) REVERT: E 141 GLU cc_start: 0.8267 (mp0) cc_final: 0.7934 (mp0) REVERT: E 149 ARG cc_start: 0.8689 (ptt-90) cc_final: 0.6727 (ptm160) REVERT: E 168 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8122 (mt-10) REVERT: F 67 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.7986 (t0) REVERT: F 96 ASP cc_start: 0.8533 (t70) cc_final: 0.8042 (t0) REVERT: F 112 ASN cc_start: 0.8264 (m-40) cc_final: 0.7852 (m110) REVERT: F 132 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7857 (mt-10) REVERT: G 16 LYS cc_start: 0.7998 (tptt) cc_final: 0.7598 (tppt) REVERT: G 82 TYR cc_start: 0.9096 (m-10) cc_final: 0.8788 (m-10) REVERT: G 108 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8353 (mm-40) REVERT: G 138 GLU cc_start: 0.8327 (tt0) cc_final: 0.7972 (tt0) REVERT: G 149 ARG cc_start: 0.9105 (ptt-90) cc_final: 0.8830 (ptt90) outliers start: 26 outliers final: 20 residues processed: 191 average time/residue: 0.7295 time to fit residues: 174.7367 Evaluate side-chains 190 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 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 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 E residue 62 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 176 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 99 optimal weight: 0.0770 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 78 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN D 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.088285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.074962 restraints weight = 36818.591| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 1.84 r_work: 0.2553 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9534 Z= 0.083 Angle : 0.468 6.525 12943 Z= 0.230 Chirality : 0.043 0.213 1428 Planarity : 0.003 0.041 1603 Dihedral : 5.179 31.757 1359 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.54 % Allowed : 16.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.27), residues: 1127 helix: 0.83 (0.33), residues: 294 sheet: -0.42 (0.28), residues: 301 loop : 1.40 (0.32), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 66 HIS 0.001 0.000 HIS B 80 PHE 0.009 0.001 PHE E 154 TYR 0.011 0.001 TYR A 35 ARG 0.008 0.000 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.02641 ( 287) hydrogen bonds : angle 3.61783 ( 819) covalent geometry : bond 0.00186 ( 9534) covalent geometry : angle 0.46813 (12943) ********************** 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 194 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 1.626 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.8963 (tp30) cc_final: 0.8626 (mm-30) REVERT: B 108 GLN cc_start: 0.8179 (mm110) cc_final: 0.7547 (mm-40) REVERT: B 109 ARG cc_start: 0.8148 (ttm110) cc_final: 0.7934 (ttp80) REVERT: C 17 GLU cc_start: 0.8091 (tt0) cc_final: 0.7627 (tp30) REVERT: C 56 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8287 (p) REVERT: C 83 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8000 (ttp80) REVERT: C 97 ARG cc_start: 0.8357 (ttm110) cc_final: 0.7901 (ttm170) REVERT: C 107 MET cc_start: 0.9241 (ttp) cc_final: 0.8939 (ttp) REVERT: C 149 ARG cc_start: 0.8929 (ptt-90) cc_final: 0.6988 (ptm-80) REVERT: D 79 ARG cc_start: 0.8687 (mtt90) cc_final: 0.8240 (mtp85) REVERT: D 95 ASN cc_start: 0.8861 (t0) cc_final: 0.8604 (t0) REVERT: D 107 MET cc_start: 0.8924 (ttp) cc_final: 0.8205 (ttp) REVERT: D 149 ARG cc_start: 0.8992 (ptt-90) cc_final: 0.7215 (ptm-80) REVERT: D 155 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8862 (tt) REVERT: E 16 LYS cc_start: 0.7646 (tptp) cc_final: 0.7292 (tptp) REVERT: E 18 MET cc_start: 0.8673 (ttt) cc_final: 0.8464 (mtp) REVERT: E 141 GLU cc_start: 0.8273 (mp0) cc_final: 0.7959 (mp0) REVERT: E 149 ARG cc_start: 0.8658 (ptt-90) cc_final: 0.6765 (ptm160) REVERT: E 168 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8076 (mt-10) REVERT: F 67 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.7900 (t0) REVERT: F 96 ASP cc_start: 0.8355 (t70) cc_final: 0.7991 (t0) REVERT: F 112 ASN cc_start: 0.8240 (m-40) cc_final: 0.7800 (m110) REVERT: F 132 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7936 (mt-10) REVERT: G 16 LYS cc_start: 0.8006 (tptt) cc_final: 0.7613 (tppt) REVERT: G 108 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8381 (mm-40) REVERT: G 138 GLU cc_start: 0.8330 (tt0) cc_final: 0.7978 (tt0) REVERT: G 149 ARG cc_start: 0.9072 (ptt-90) cc_final: 0.8820 (ptt90) outliers start: 15 outliers final: 9 residues processed: 192 average time/residue: 0.7552 time to fit residues: 180.3622 Evaluate side-chains 182 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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 C residue 56 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 176 SER 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 14 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.090867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.077179 restraints weight = 36701.955| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 1.92 r_work: 0.2523 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2398 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 9534 Z= 0.193 Angle : 0.540 7.608 12943 Z= 0.266 Chirality : 0.046 0.213 1428 Planarity : 0.004 0.045 1603 Dihedral : 5.539 36.041 1357 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.06 % Allowed : 16.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 1127 helix: 0.61 (0.33), residues: 294 sheet: -0.70 (0.28), residues: 287 loop : 1.37 (0.31), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 153 HIS 0.003 0.001 HIS G 80 PHE 0.017 0.002 PHE F 154 TYR 0.015 0.001 TYR F 35 ARG 0.007 0.001 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 287) hydrogen bonds : angle 3.91518 ( 819) covalent geometry : bond 0.00453 ( 9534) covalent geometry : angle 0.54008 (12943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10648.93 seconds wall clock time: 185 minutes 56.40 seconds (11156.40 seconds total)