Starting phenix.real_space_refine on Mon May 19 11:41:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s5e_19733/05_2025/8s5e_19733_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s5e_19733/05_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_19733/05_2025/8s5e_19733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s5e_19733/05_2025/8s5e_19733.map" model { file = "/net/cci-nas-00/data/ceres_data/8s5e_19733/05_2025/8s5e_19733_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s5e_19733/05_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-5687/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: 8.61, per 1000 atoms: 0.47 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: 4.67 Conformation dependent library (CDL) restraints added in 1.3 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: 1.37 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: 5.72 Time building geometry restraints manager: 5.55 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.280 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 37.390 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.700 ------------------------------------------------------------------------------- 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 : 1.441 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: 0.6002 time to fit residues: 225.3535 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 : 1.367 ------------------------------------------------------------------------------- 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 = 0.089175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.076122 restraints weight = 36382.625| |-----------------------------------------------------------------------------| 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: 0.8424 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 : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.9105 (tptp) cc_final: 0.8904 (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: 0.8504 (mm-30) REVERT: B 113 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7837 (mm-30) REVERT: B 118 ASN cc_start: 0.8916 (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: 0.8437 (p0) cc_final: 0.8111 (p0) REVERT: C 59 LYS cc_start: 0.7796 (mtpp) cc_final: 0.7556 (mtpt) REVERT: C 67 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8297 (t0) REVERT: C 71 GLN cc_start: 0.8615 (mt0) cc_final: 0.8376 (mt0) REVERT: C 83 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7771 (ttp80) REVERT: C 97 ARG cc_start: 0.8349 (ttm110) cc_final: 0.7993 (ttm170) REVERT: C 107 MET cc_start: 0.9268 (ttp) cc_final: 0.8784 (ttp) REVERT: C 149 ARG cc_start: 0.9047 (ptt-90) cc_final: 0.7600 (ptm-80) REVERT: C 171 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8403 (mm-30) REVERT: D 18 MET cc_start: 0.8699 (ttt) cc_final: 0.8205 (ttt) REVERT: D 26 ASP cc_start: 0.9199 (p0) cc_final: 0.8990 (p0) REVERT: D 83 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7798 (ttm-80) REVERT: D 107 MET cc_start: 0.9116 (ttp) cc_final: 0.8245 (ttp) REVERT: D 110 MET cc_start: 0.8756 (ttp) cc_final: 0.8551 (ttm) REVERT: D 149 ARG cc_start: 0.9110 (ptt-90) cc_final: 0.7405 (ptm-80) REVERT: E 18 MET cc_start: 0.8608 (ttt) cc_final: 0.8210 (ttt) REVERT: E 110 MET cc_start: 0.9102 (ttp) cc_final: 0.8890 (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: 0.8132 (mt-10) REVERT: F 56 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8322 (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: 0.7950 (t0) REVERT: F 161 THR cc_start: 0.8139 (p) cc_final: 0.7909 (p) REVERT: G 16 LYS cc_start: 0.7918 (tptt) cc_final: 0.7570 (tppt) REVERT: G 107 MET cc_start: 0.8973 (ttp) cc_final: 0.8737 (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: 0.8783 (t0) REVERT: G 138 GLU cc_start: 0.8270 (tt0) cc_final: 0.7934 (tt0) REVERT: G 142 LYS cc_start: 0.8494 (mttp) cc_final: 0.8277 (mttp) outliers start: 19 outliers final: 11 residues processed: 199 average time/residue: 0.7187 time to fit residues: 179.3609 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 : 1.389 ------------------------------------------------------------------------------- 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: 0.7980 chunk 96 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.2793 r_free = 0.2793 target = 0.085291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.072550 restraints weight = 37377.361| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 1.75 r_work: 0.2498 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2376 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 9534 Z= 0.203 Angle : 0.572 8.002 12943 Z= 0.281 Chirality : 0.046 0.173 1428 Planarity : 0.004 0.043 1603 Dihedral : 6.319 38.725 1367 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.85 % Allowed : 14.49 % 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: 0.35 (0.28), residues: 1127 helix: -0.38 (0.30), residues: 294 sheet: -0.93 (0.26), residues: 322 loop : 1.82 (0.34), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 66 HIS 0.004 0.001 HIS G 80 PHE 0.023 0.002 PHE F 154 TYR 0.013 0.002 TYR E 35 ARG 0.004 0.001 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 287) hydrogen bonds : angle 4.29875 ( 819) covalent geometry : bond 0.00470 ( 9534) covalent geometry : angle 0.57220 (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 201 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7707 (mp) REVERT: A 171 GLU cc_start: 0.8781 (tp30) cc_final: 0.8405 (mm-30) REVERT: B 79 ARG cc_start: 0.8234 (mtt-85) cc_final: 0.7906 (mtt180) REVERT: B 113 GLU cc_start: 0.8642 (mm-30) cc_final: 0.7857 (mm-30) REVERT: C 83 ARG cc_start: 0.8342 (ttp80) cc_final: 0.7999 (ttp80) REVERT: C 97 ARG cc_start: 0.8331 (ttm110) cc_final: 0.8060 (ttm110) REVERT: C 107 MET cc_start: 0.9295 (ttp) cc_final: 0.8857 (ttp) REVERT: C 149 ARG cc_start: 0.9010 (ptt-90) cc_final: 0.7414 (ptm-80) REVERT: C 171 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8510 (mm-30) REVERT: D 18 MET cc_start: 0.8766 (ttt) cc_final: 0.8441 (ttt) REVERT: D 46 ILE cc_start: 0.8717 (pt) cc_final: 0.8473 (pt) REVERT: D 83 ARG cc_start: 0.8508 (ttp80) cc_final: 0.8145 (ttm-80) REVERT: D 107 MET cc_start: 0.9010 (ttp) cc_final: 0.7994 (ttp) REVERT: D 129 ASP cc_start: 0.8849 (p0) cc_final: 0.8592 (p0) REVERT: D 149 ARG cc_start: 0.9077 (ptt-90) cc_final: 0.7315 (ptm-80) REVERT: E 18 MET cc_start: 0.8750 (ttt) cc_final: 0.8379 (ttt) REVERT: E 110 MET cc_start: 0.9189 (ttp) cc_final: 0.8918 (ttm) REVERT: E 141 GLU cc_start: 0.8330 (mp0) cc_final: 0.7901 (mp0) REVERT: E 149 ARG cc_start: 0.8665 (ptt-90) cc_final: 0.6915 (ptm160) REVERT: E 168 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8114 (mt-10) REVERT: F 56 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8286 (p) REVERT: F 67 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.7979 (t0) REVERT: F 79 ARG cc_start: 0.8362 (mtt-85) cc_final: 0.8098 (mtt-85) REVERT: F 96 ASP cc_start: 0.8523 (t70) cc_final: 0.8013 (t0) REVERT: F 132 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7941 (mt-10) REVERT: G 16 LYS cc_start: 0.7996 (tptt) cc_final: 0.7583 (tppt) REVERT: G 108 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8277 (mm-40) REVERT: G 138 GLU cc_start: 0.8470 (tt0) cc_final: 0.7990 (tt0) outliers start: 18 outliers final: 14 residues processed: 198 average time/residue: 0.7598 time to fit residues: 186.1622 Evaluate side-chains 182 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 1.590 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 15 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.2803 r_free = 0.2803 target = 0.086006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.072953 restraints weight = 37332.091| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 1.81 r_work: 0.2495 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2373 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9534 Z= 0.182 Angle : 0.537 7.272 12943 Z= 0.266 Chirality : 0.045 0.173 1428 Planarity : 0.004 0.040 1603 Dihedral : 6.074 39.036 1365 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: 0.49 (0.27), residues: 1127 helix: 0.09 (0.31), residues: 294 sheet: -0.88 (0.27), residues: 322 loop : 1.69 (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 0.022 0.002 PHE F 154 TYR 0.011 0.001 TYR C 35 ARG 0.004 0.000 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 287) hydrogen bonds : angle 4.10956 ( 819) covalent geometry : bond 0.00418 ( 9534) covalent geometry : angle 0.53652 (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 : 1.371 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 171 GLU cc_start: 0.8996 (tp30) cc_final: 0.8642 (mm-30) REVERT: B 108 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8072 (mm110) REVERT: B 113 GLU cc_start: 0.8675 (mm-30) cc_final: 0.7800 (mm-30) REVERT: C 67 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8417 (t0) REVERT: C 83 ARG cc_start: 0.8420 (ttp80) cc_final: 0.7983 (ttp80) REVERT: C 97 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7848 (ttm170) REVERT: C 107 MET cc_start: 0.9256 (ttp) cc_final: 0.8864 (ttp) REVERT: C 149 ARG cc_start: 0.8944 (ptt-90) cc_final: 0.7362 (ptm-80) REVERT: D 57 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8588 (mp10) REVERT: D 107 MET cc_start: 0.8963 (ttp) cc_final: 0.7989 (ttp) REVERT: D 129 ASP cc_start: 0.8923 (p0) cc_final: 0.8671 (p0) REVERT: D 149 ARG cc_start: 0.9043 (ptt-90) cc_final: 0.7246 (ptm-80) REVERT: E 16 LYS cc_start: 0.7607 (tptp) cc_final: 0.7214 (tptm) REVERT: E 18 MET cc_start: 0.8770 (ttt) cc_final: 0.8405 (ttt) REVERT: E 110 MET cc_start: 0.9247 (ttp) cc_final: 0.8990 (ttm) REVERT: E 141 GLU cc_start: 0.8262 (mp0) cc_final: 0.7950 (mp0) REVERT: E 149 ARG cc_start: 0.8620 (ptt-90) cc_final: 0.6892 (ptm160) REVERT: E 168 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8070 (mt-10) REVERT: F 56 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8301 (p) REVERT: F 67 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8254 (t0) REVERT: F 79 ARG cc_start: 0.8344 (mtt-85) cc_final: 0.8138 (mtt-85) REVERT: F 96 ASP cc_start: 0.8431 (t70) cc_final: 0.7875 (t0) REVERT: F 132 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7874 (mt-10) REVERT: G 16 LYS cc_start: 0.8029 (tptt) cc_final: 0.7637 (tppt) REVERT: G 108 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8369 (mm-40) REVERT: G 149 ARG cc_start: 0.8995 (ptt90) cc_final: 0.8587 (ptt90) outliers start: 28 outliers final: 22 residues processed: 197 average time/residue: 0.7630 time to fit residues: 187.1342 Evaluate side-chains 192 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 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 D residue 158 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 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 62 SER 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: 0.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 50 optimal weight: 0.0060 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 = 0.2806 r_free = 0.2806 target = 0.086245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.073144 restraints weight = 37643.969| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 1.83 r_work: 0.2499 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2377 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 9534 Z= 0.157 Angle : 0.519 7.290 12943 Z= 0.256 Chirality : 0.044 0.170 1428 Planarity : 0.004 0.039 1603 Dihedral : 5.887 38.149 1365 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.88 % Allowed : 14.90 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.27), residues: 1127 helix: 0.36 (0.32), residues: 294 sheet: -0.80 (0.27), residues: 322 loop : 1.55 (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 0.018 0.002 PHE F 154 TYR 0.012 0.001 TYR E 35 ARG 0.004 0.000 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 287) hydrogen bonds : angle 3.98268 ( 819) covalent geometry : bond 0.00361 ( 9534) covalent geometry : angle 0.51923 (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: 28 poor density : 169 time to evaluate : 1.371 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7859 (mp) REVERT: A 171 GLU cc_start: 0.9001 (tp30) cc_final: 0.8642 (mm-30) REVERT: B 113 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8187 (mm-30) REVERT: C 67 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8406 (t0) REVERT: C 83 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8000 (ttp80) REVERT: C 97 ARG cc_start: 0.8325 (ttm110) cc_final: 0.7908 (ttm170) REVERT: C 107 MET cc_start: 0.9227 (ttp) cc_final: 0.8878 (ttp) REVERT: C 149 ARG cc_start: 0.8947 (ptt-90) cc_final: 0.7343 (ptm-80) REVERT: D 79 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8141 (mtp85) REVERT: D 107 MET cc_start: 0.8956 (ttp) cc_final: 0.7998 (ttp) REVERT: D 149 ARG cc_start: 0.9028 (ptt-90) cc_final: 0.7215 (ptm-80) REVERT: D 155 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8948 (tt) REVERT: D 171 GLU cc_start: 0.8850 (tp30) cc_final: 0.8387 (tt0) REVERT: E 16 LYS cc_start: 0.7616 (tptp) cc_final: 0.7176 (tptm) REVERT: E 141 GLU cc_start: 0.8251 (mp0) cc_final: 0.7928 (mp0) REVERT: E 149 ARG cc_start: 0.8617 (ptt-90) cc_final: 0.6858 (ptm160) REVERT: E 168 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8099 (mt-10) REVERT: F 67 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8358 (t0) REVERT: F 96 ASP cc_start: 0.8523 (t70) cc_final: 0.7968 (t0) REVERT: F 112 ASN cc_start: 0.8248 (m-40) cc_final: 0.7755 (m110) REVERT: F 132 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7887 (mt-10) REVERT: G 16 LYS cc_start: 0.8011 (tptt) cc_final: 0.7613 (tppt) REVERT: G 108 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8390 (mm-40) REVERT: G 149 ARG cc_start: 0.8983 (ptt90) cc_final: 0.8590 (ptt90) outliers start: 28 outliers final: 17 residues processed: 191 average time/residue: 0.7472 time to fit residues: 178.7657 Evaluate side-chains 188 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 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 79 ARG Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.2819 r_free = 0.2819 target = 0.086994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.073898 restraints weight = 37357.099| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 1.80 r_work: 0.2508 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2385 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3662 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= 0.138 Angle : 0.504 7.091 12943 Z= 0.248 Chirality : 0.044 0.177 1428 Planarity : 0.003 0.038 1603 Dihedral : 5.630 36.908 1361 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.77 % Allowed : 15.01 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.27), residues: 1127 helix: 0.50 (0.32), residues: 294 sheet: -0.75 (0.27), residues: 322 loop : 1.58 (0.32), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 66 HIS 0.002 0.000 HIS G 80 PHE 0.015 0.001 PHE F 154 TYR 0.012 0.001 TYR C 35 ARG 0.005 0.000 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 287) hydrogen bonds : angle 3.88609 ( 819) covalent geometry : bond 0.00316 ( 9534) covalent geometry : angle 0.50358 (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 194 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7828 (mp) REVERT: A 171 GLU cc_start: 0.8941 (tp30) cc_final: 0.8574 (mm-30) REVERT: B 108 GLN cc_start: 0.8086 (mm110) cc_final: 0.7394 (mm-40) REVERT: B 113 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8198 (mm-30) REVERT: C 67 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8436 (t0) REVERT: C 83 ARG cc_start: 0.8432 (ttp80) cc_final: 0.7977 (ttp80) REVERT: C 97 ARG cc_start: 0.8329 (ttm110) cc_final: 0.7895 (ttm170) REVERT: C 107 MET cc_start: 0.9211 (ttp) cc_final: 0.8866 (ttp) REVERT: C 149 ARG cc_start: 0.8945 (ptt-90) cc_final: 0.7313 (ptm-80) REVERT: D 79 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8113 (mtp85) REVERT: D 107 MET cc_start: 0.8911 (ttp) cc_final: 0.7947 (ttp) REVERT: D 149 ARG cc_start: 0.9027 (ptt-90) cc_final: 0.7206 (ptm-80) REVERT: D 155 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8934 (tt) REVERT: E 16 LYS cc_start: 0.7609 (tptp) cc_final: 0.7155 (tptm) REVERT: E 141 GLU cc_start: 0.8249 (mp0) cc_final: 0.7917 (mp0) REVERT: E 149 ARG cc_start: 0.8653 (ptt-90) cc_final: 0.6836 (ptm160) REVERT: E 168 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8099 (mt-10) REVERT: F 67 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.7928 (t0) REVERT: F 96 ASP cc_start: 0.8484 (t70) cc_final: 0.7940 (t0) REVERT: F 112 ASN cc_start: 0.8218 (m-40) cc_final: 0.7728 (m110) REVERT: F 132 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7944 (mt-10) REVERT: G 16 LYS cc_start: 0.7987 (tptt) cc_final: 0.7579 (tppt) REVERT: G 108 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8360 (mm-40) REVERT: G 149 ARG cc_start: 0.8945 (ptt90) cc_final: 0.8532 (ptt90) outliers start: 27 outliers final: 18 residues processed: 189 average time/residue: 0.7254 time to fit residues: 170.8054 Evaluate side-chains 189 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain 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 79 ARG Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 85 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 110 optimal weight: 0.0570 chunk 84 optimal weight: 0.0980 chunk 73 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.2825 r_free = 0.2825 target = 0.087237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.074324 restraints weight = 37102.105| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 1.77 r_work: 0.2515 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2392 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3718 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= 0.137 Angle : 0.503 7.131 12943 Z= 0.248 Chirality : 0.044 0.183 1428 Planarity : 0.003 0.039 1603 Dihedral : 5.519 36.396 1359 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.57 % Allowed : 15.52 % 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: 0.69 (0.27), residues: 1127 helix: 0.59 (0.33), residues: 294 sheet: -0.74 (0.27), residues: 322 loop : 1.56 (0.32), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 172 HIS 0.002 0.000 HIS G 80 PHE 0.014 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 0.03017 ( 287) hydrogen bonds : angle 3.84823 ( 819) covalent geometry : bond 0.00314 ( 9534) covalent geometry : angle 0.50319 (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 192 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7817 (mp) REVERT: A 171 GLU cc_start: 0.8949 (tp30) cc_final: 0.8577 (mm-30) REVERT: B 108 GLN cc_start: 0.8158 (mm110) cc_final: 0.7508 (mm-40) REVERT: B 113 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8180 (mm-30) REVERT: C 67 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8428 (t0) REVERT: C 83 ARG cc_start: 0.8428 (ttp80) cc_final: 0.7962 (ttp80) REVERT: C 107 MET cc_start: 0.9203 (ttp) cc_final: 0.8860 (ttp) REVERT: C 149 ARG cc_start: 0.8918 (ptt-90) cc_final: 0.7246 (ptm-80) REVERT: D 79 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8109 (mtp85) REVERT: D 107 MET cc_start: 0.8899 (ttp) cc_final: 0.7939 (ttp) REVERT: D 149 ARG cc_start: 0.9019 (ptt-90) cc_final: 0.7202 (ptm-80) REVERT: D 155 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8929 (tt) REVERT: D 171 GLU cc_start: 0.8814 (tp30) cc_final: 0.8322 (tt0) REVERT: E 16 LYS cc_start: 0.7608 (tptp) cc_final: 0.7187 (tptp) REVERT: E 141 GLU cc_start: 0.8246 (mp0) cc_final: 0.7940 (mp0) REVERT: E 149 ARG cc_start: 0.8647 (ptt-90) cc_final: 0.6833 (ptm160) REVERT: E 168 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8083 (mt-10) REVERT: F 67 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.7929 (t0) REVERT: F 96 ASP cc_start: 0.8505 (t70) cc_final: 0.7968 (t0) REVERT: F 112 ASN cc_start: 0.8220 (m-40) cc_final: 0.7742 (m110) REVERT: F 132 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7941 (mt-10) REVERT: G 16 LYS cc_start: 0.7975 (tptt) cc_final: 0.7567 (tppt) REVERT: G 82 TYR cc_start: 0.9084 (m-10) cc_final: 0.8841 (m-10) REVERT: G 108 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8357 (mm-40) REVERT: G 149 ARG cc_start: 0.8898 (ptt90) cc_final: 0.8481 (ptt90) outliers start: 25 outliers final: 19 residues processed: 188 average time/residue: 0.7232 time to fit residues: 170.8512 Evaluate side-chains 189 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 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 79 ARG Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.2819 r_free = 0.2819 target = 0.086945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.073923 restraints weight = 37248.760| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 1.79 r_work: 0.2510 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2387 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 9534 Z= 0.153 Angle : 0.512 7.202 12943 Z= 0.252 Chirality : 0.044 0.190 1428 Planarity : 0.004 0.044 1603 Dihedral : 5.550 36.724 1359 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.08 % Allowed : 14.90 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.65 (0.27), residues: 1127 helix: 0.60 (0.33), residues: 294 sheet: -0.78 (0.26), residues: 322 loop : 1.50 (0.32), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 172 HIS 0.002 0.000 HIS G 80 PHE 0.015 0.002 PHE F 154 TYR 0.011 0.001 TYR E 35 ARG 0.006 0.000 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.03069 ( 287) hydrogen bonds : angle 3.87857 ( 819) covalent geometry : bond 0.00352 ( 9534) covalent geometry : angle 0.51160 (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 198 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 1.371 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7828 (mp) REVERT: A 171 GLU cc_start: 0.8954 (tp30) cc_final: 0.8579 (mm-30) REVERT: B 108 GLN cc_start: 0.8185 (mm110) cc_final: 0.7792 (mm-40) REVERT: B 113 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8179 (mm-30) REVERT: C 67 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8478 (t0) REVERT: C 83 ARG cc_start: 0.8412 (ttp80) cc_final: 0.7968 (ttp80) REVERT: C 107 MET cc_start: 0.9221 (ttp) cc_final: 0.8881 (ttp) REVERT: C 149 ARG cc_start: 0.8919 (ptt-90) cc_final: 0.7241 (ptm-80) REVERT: D 79 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8126 (mtp85) REVERT: D 107 MET cc_start: 0.8915 (ttp) cc_final: 0.7957 (ttp) REVERT: D 149 ARG cc_start: 0.9023 (ptt-90) cc_final: 0.7217 (ptm-80) REVERT: D 155 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8952 (tt) REVERT: D 171 GLU cc_start: 0.8821 (tp30) cc_final: 0.8334 (tt0) REVERT: E 16 LYS cc_start: 0.7631 (tptp) cc_final: 0.7203 (tptp) REVERT: E 141 GLU cc_start: 0.8257 (mp0) cc_final: 0.7917 (mp0) REVERT: E 149 ARG cc_start: 0.8623 (ptt-90) cc_final: 0.6725 (ptm160) REVERT: E 168 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8092 (mt-10) REVERT: F 67 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.7941 (t0) REVERT: F 96 ASP cc_start: 0.8434 (t70) cc_final: 0.7901 (t0) REVERT: F 112 ASN cc_start: 0.8226 (m-40) cc_final: 0.7750 (m110) REVERT: F 132 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7946 (mt-10) REVERT: G 16 LYS cc_start: 0.7990 (tptt) cc_final: 0.7583 (tppt) REVERT: G 82 TYR cc_start: 0.9109 (m-10) cc_final: 0.8792 (m-10) REVERT: G 108 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8363 (mm-40) REVERT: G 149 ARG cc_start: 0.8894 (ptt90) cc_final: 0.8498 (ptt90) outliers start: 30 outliers final: 21 residues processed: 192 average time/residue: 0.7026 time to fit residues: 168.3368 Evaluate side-chains 190 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 79 ARG Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 80 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.2820 r_free = 0.2820 target = 0.086991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.074076 restraints weight = 37318.475| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 1.78 r_work: 0.2515 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2392 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 9534 Z= 0.129 Angle : 0.497 7.122 12943 Z= 0.244 Chirality : 0.044 0.194 1428 Planarity : 0.003 0.044 1603 Dihedral : 5.452 35.857 1359 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.67 % Allowed : 15.31 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.33), residues: 294 sheet: -0.74 (0.27), residues: 322 loop : 1.53 (0.32), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 0.02938 ( 287) hydrogen bonds : angle 3.80812 ( 819) covalent geometry : bond 0.00296 ( 9534) covalent geometry : angle 0.49685 (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 191 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.538 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7821 (mp) REVERT: A 171 GLU cc_start: 0.8956 (tp30) cc_final: 0.8587 (mm-30) REVERT: B 108 GLN cc_start: 0.8158 (mm110) cc_final: 0.7786 (mm-40) REVERT: C 56 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8264 (p) REVERT: C 67 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8474 (t0) REVERT: C 83 ARG cc_start: 0.8428 (ttp80) cc_final: 0.7990 (ttp80) REVERT: C 107 MET cc_start: 0.9199 (ttp) cc_final: 0.8858 (ttp) REVERT: C 149 ARG cc_start: 0.8928 (ptt-90) cc_final: 0.7228 (ptm-80) REVERT: D 79 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8118 (mtp85) REVERT: D 107 MET cc_start: 0.8933 (ttp) cc_final: 0.7986 (ttp) REVERT: D 149 ARG cc_start: 0.9016 (ptt-90) cc_final: 0.7207 (ptm-80) REVERT: D 155 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8926 (tt) REVERT: D 171 GLU cc_start: 0.8805 (tp30) cc_final: 0.8218 (tt0) REVERT: E 16 LYS cc_start: 0.7634 (tptp) cc_final: 0.7201 (tptp) REVERT: E 141 GLU cc_start: 0.8255 (mp0) cc_final: 0.7944 (mp0) REVERT: E 149 ARG cc_start: 0.8667 (ptt-90) cc_final: 0.6698 (ptm160) REVERT: E 168 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8085 (mt-10) REVERT: F 67 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.7933 (t0) REVERT: F 96 ASP cc_start: 0.8436 (t70) cc_final: 0.7901 (t0) REVERT: F 112 ASN cc_start: 0.8213 (m-40) cc_final: 0.7740 (m110) REVERT: F 132 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7933 (mt-10) REVERT: G 16 LYS cc_start: 0.7983 (tptt) cc_final: 0.7576 (tppt) REVERT: G 108 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8359 (mm-40) REVERT: G 149 ARG cc_start: 0.8870 (ptt90) cc_final: 0.8480 (ptt90) outliers start: 26 outliers final: 19 residues processed: 186 average time/residue: 0.7300 time to fit residues: 169.9071 Evaluate side-chains 188 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 91 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 ARG 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 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 79 ARG Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain 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 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: 0.9980 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 58 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.2842 r_free = 0.2842 target = 0.087684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.074265 restraints weight = 37172.065| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 1.87 r_work: 0.2546 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2421 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3809 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= 0.118 Angle : 0.489 6.932 12943 Z= 0.240 Chirality : 0.044 0.208 1428 Planarity : 0.003 0.044 1603 Dihedral : 5.369 34.395 1359 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.67 % Allowed : 15.11 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.78 (0.27), residues: 1127 helix: 0.74 (0.33), residues: 294 sheet: -0.71 (0.27), residues: 322 loop : 1.57 (0.33), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 66 HIS 0.001 0.000 HIS G 80 PHE 0.011 0.001 PHE E 154 TYR 0.012 0.001 TYR C 35 ARG 0.008 0.000 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.02855 ( 287) hydrogen bonds : angle 3.73794 ( 819) covalent geometry : bond 0.00269 ( 9534) covalent geometry : angle 0.48900 (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 193 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 1.456 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.9025 (tp30) cc_final: 0.8668 (mm-30) REVERT: B 108 GLN cc_start: 0.8123 (mm110) cc_final: 0.7722 (mm-40) REVERT: C 17 GLU cc_start: 0.8039 (tt0) cc_final: 0.7505 (tp30) REVERT: C 56 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8251 (p) REVERT: C 67 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8446 (t0) REVERT: C 83 ARG cc_start: 0.8413 (ttp80) cc_final: 0.7976 (ttp80) REVERT: C 107 MET cc_start: 0.9238 (ttp) cc_final: 0.8925 (ttp) REVERT: C 149 ARG cc_start: 0.8884 (ptt-90) cc_final: 0.7218 (ptm-80) REVERT: D 79 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8144 (mtp85) REVERT: D 107 MET cc_start: 0.8942 (ttp) cc_final: 0.7955 (ttp) REVERT: D 149 ARG cc_start: 0.8993 (ptt-90) cc_final: 0.7205 (ptm-80) REVERT: D 155 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8926 (tt) REVERT: E 16 LYS cc_start: 0.7640 (tptp) cc_final: 0.7193 (tptp) REVERT: E 141 GLU cc_start: 0.8264 (mp0) cc_final: 0.7936 (mp0) REVERT: E 149 ARG cc_start: 0.8638 (ptt-90) cc_final: 0.6753 (ptm160) REVERT: E 168 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8101 (mt-10) REVERT: F 67 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.7925 (t0) REVERT: F 96 ASP cc_start: 0.8432 (t70) cc_final: 0.7926 (t0) REVERT: F 112 ASN cc_start: 0.8229 (m-40) cc_final: 0.7782 (m110) REVERT: F 132 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7924 (mt-10) REVERT: G 16 LYS cc_start: 0.7976 (tptt) cc_final: 0.7575 (tppt) REVERT: G 108 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8356 (mm-40) REVERT: G 149 ARG cc_start: 0.8885 (ptt90) cc_final: 0.8509 (ptt90) outliers start: 26 outliers final: 20 residues processed: 188 average time/residue: 0.7219 time to fit residues: 169.9220 Evaluate side-chains 189 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain 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 62 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 96 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 66 optimal weight: 0.0770 chunk 62 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.2849 r_free = 0.2849 target = 0.088022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.074641 restraints weight = 37109.431| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 1.86 r_work: 0.2544 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2420 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9534 Z= 0.138 Angle : 0.502 7.174 12943 Z= 0.247 Chirality : 0.044 0.214 1428 Planarity : 0.003 0.043 1603 Dihedral : 5.392 34.584 1359 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.88 % Allowed : 15.31 % 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: 0.71 (0.27), residues: 1127 helix: 0.71 (0.33), residues: 294 sheet: -0.75 (0.27), residues: 322 loop : 1.51 (0.32), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 172 HIS 0.001 0.000 HIS G 80 PHE 0.014 0.001 PHE F 154 TYR 0.012 0.001 TYR D 35 ARG 0.007 0.000 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.02935 ( 287) hydrogen bonds : angle 3.78021 ( 819) covalent geometry : bond 0.00317 ( 9534) covalent geometry : angle 0.50182 (12943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9244.24 seconds wall clock time: 159 minutes 5.08 seconds (9545.08 seconds total)