Starting phenix.real_space_refine on Thu Feb 22 07:23:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy7_22523/02_2024/7jy7_22523_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy7_22523/02_2024/7jy7_22523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy7_22523/02_2024/7jy7_22523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy7_22523/02_2024/7jy7_22523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy7_22523/02_2024/7jy7_22523_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy7_22523/02_2024/7jy7_22523_trim_updated.pdb" } resolution = 2.9 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= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 49456 atoms to isotropic. 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 150 5.49 5 Mg 9 5.21 5 S 116 5.16 5 C 15315 2.51 5 N 4329 2.21 5 O 5199 1.98 5 H 24338 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 18": "OE1" <-> "OE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B ASP 48": "OD1" <-> "OD2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ASP 161": "OD1" <-> "OD2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B ASP 311": "OD1" <-> "OD2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D GLU 285": "OE1" <-> "OE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 100": "OD1" <-> "OD2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "E PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 266": "OE1" <-> "OE2" Residue "E GLU 285": "OE1" <-> "OE2" Residue "E GLU 318": "OE1" <-> "OE2" Residue "F GLU 4": "OE1" <-> "OE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 68": "OE1" <-> "OE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 100": "OD1" <-> "OD2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F GLU 285": "OE1" <-> "OE2" Residue "F GLU 314": "OE1" <-> "OE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G GLU 18": "OE1" <-> "OE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ASP 32": "OD1" <-> "OD2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "G GLU 86": "OE1" <-> "OE2" Residue "G PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 100": "OD1" <-> "OD2" Residue "G ASP 110": "OD1" <-> "OD2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G GLU 156": "OE1" <-> "OE2" Residue "G PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G GLU 285": "OE1" <-> "OE2" Residue "G ASP 311": "OD1" <-> "OD2" Residue "G GLU 314": "OE1" <-> "OE2" Residue "G GLU 318": "OE1" <-> "OE2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 100": "OD1" <-> "OD2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H GLU 154": "OE1" <-> "OE2" Residue "H GLU 158": "OE1" <-> "OE2" Residue "H ASP 161": "OD1" <-> "OD2" Residue "H PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 235": "OE1" <-> "OE2" Residue "H GLU 285": "OE1" <-> "OE2" Residue "H TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 318": "OE1" <-> "OE2" Residue "I ASP 36": "OD1" <-> "OD2" Residue "I ASP 48": "OD1" <-> "OD2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I GLU 86": "OE1" <-> "OE2" Residue "I PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 127": "OE1" <-> "OE2" Residue "I GLU 154": "OE1" <-> "OE2" Residue "I GLU 158": "OE1" <-> "OE2" Residue "I ASP 161": "OD1" <-> "OD2" Residue "I PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 233": "OE1" <-> "OE2" Residue "I GLU 266": "OE1" <-> "OE2" Residue "I GLU 281": "OE1" <-> "OE2" Residue "I GLU 285": "OE1" <-> "OE2" Residue "I GLU 314": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 49456 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "B" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "C" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "D" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "E" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "F" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "G" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "H" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "I" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4575 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain: "S" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 854 Classifications: {'DNA': 27} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 26} Chain: "T" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1530 Classifications: {'DNA': 48} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 47} Chain: "U" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1529 Classifications: {'DNA': 48} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 47} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.76, per 1000 atoms: 0.38 Number of scatterers: 49456 At special positions: 0 Unit cell: (137, 123.848, 199.472, 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 116 16.00 P 150 15.00 Mg 9 11.99 O 5199 8.00 N 4329 7.00 C 15315 6.00 H 24338 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 - 3.50 Amino acid : False - 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: 31.23 Conformation dependent library (CDL) restraints added in 3.8 seconds 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5324 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 36 sheets defined 39.0% alpha, 19.2% beta 46 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 19.87 Creating SS restraints... Processing helix chain 'A' and resid 2 through 21 removed outlier: 4.072A pdb=" N LYS A 6 " --> pdb=" O ILE A 2 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 72 through 86 removed outlier: 3.617A pdb=" N GLU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 122 through 135 Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 166 through 183 removed outlier: 3.559A pdb=" N ARG A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLY A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 270 through 280 removed outlier: 3.588A pdb=" N ASP A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 327 Processing helix chain 'B' and resid 2 through 21 removed outlier: 4.031A pdb=" N LYS B 6 " --> pdb=" O ILE B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 45 through 51 Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 166 through 185 removed outlier: 4.648A pdb=" N GLY B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 270 through 280 Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 327 Processing helix chain 'C' and resid 2 through 21 removed outlier: 3.811A pdb=" N LYS C 6 " --> pdb=" O ILE C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 45 through 51 Processing helix chain 'C' and resid 72 through 86 removed outlier: 3.788A pdb=" N GLU C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 122 through 135 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 166 through 185 removed outlier: 4.782A pdb=" N GLY C 180 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.524A pdb=" N ASP C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 311 Processing helix chain 'C' and resid 313 through 327 Processing helix chain 'D' and resid 4 through 21 Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 33 through 35 No H-bonds generated for 'chain 'D' and resid 33 through 35' Processing helix chain 'D' and resid 45 through 51 Processing helix chain 'D' and resid 72 through 85 Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 152 through 156 Processing helix chain 'D' and resid 166 through 185 removed outlier: 4.474A pdb=" N GLY D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN D 181 " --> pdb=" O LYS D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 218 Processing helix chain 'D' and resid 270 through 280 Processing helix chain 'D' and resid 302 through 311 Processing helix chain 'D' and resid 313 through 327 Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.832A pdb=" N LYS E 6 " --> pdb=" O ILE E 2 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 45 through 51 Processing helix chain 'E' and resid 72 through 85 Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'E' and resid 166 through 185 removed outlier: 3.592A pdb=" N ARG E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY E 180 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN E 181 " --> pdb=" O LYS E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 218 Processing helix chain 'E' and resid 270 through 280 removed outlier: 3.520A pdb=" N ASP E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 311 Processing helix chain 'E' and resid 313 through 327 Processing helix chain 'F' and resid 2 through 20 removed outlier: 4.019A pdb=" N LYS F 6 " --> pdb=" O ILE F 2 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 33 through 35 No H-bonds generated for 'chain 'F' and resid 33 through 35' Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 72 through 85 Processing helix chain 'F' and resid 101 through 107 Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 152 through 156 Processing helix chain 'F' and resid 166 through 184 removed outlier: 4.574A pdb=" N GLY F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN F 181 " --> pdb=" O LYS F 177 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS F 183 " --> pdb=" O ALA F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 218 Processing helix chain 'F' and resid 270 through 280 removed outlier: 3.586A pdb=" N ASP F 276 " --> pdb=" O GLY F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 311 removed outlier: 3.523A pdb=" N ASP F 311 " --> pdb=" O ALA F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 327 Processing helix chain 'G' and resid 2 through 21 removed outlier: 3.711A pdb=" N LYS G 6 " --> pdb=" O ILE G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 33 through 35 No H-bonds generated for 'chain 'G' and resid 33 through 35' Processing helix chain 'G' and resid 45 through 51 Processing helix chain 'G' and resid 72 through 85 Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 122 through 135 Processing helix chain 'G' and resid 152 through 155 No H-bonds generated for 'chain 'G' and resid 152 through 155' Processing helix chain 'G' and resid 166 through 185 removed outlier: 4.667A pdb=" N GLY G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 218 Processing helix chain 'G' and resid 270 through 281 removed outlier: 3.527A pdb=" N ASP G 276 " --> pdb=" O GLY G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 311 Processing helix chain 'G' and resid 313 through 327 removed outlier: 3.540A pdb=" N LYS G 317 " --> pdb=" O PRO G 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 20 removed outlier: 4.213A pdb=" N LYS H 6 " --> pdb=" O ILE H 2 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS H 8 " --> pdb=" O GLU H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 45 through 50 Processing helix chain 'H' and resid 72 through 85 Processing helix chain 'H' and resid 101 through 106 Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 152 through 156 Processing helix chain 'H' and resid 166 through 185 removed outlier: 3.656A pdb=" N ARG H 176 " --> pdb=" O SER H 172 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS H 177 " --> pdb=" O GLN H 173 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY H 180 " --> pdb=" O ARG H 176 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN H 181 " --> pdb=" O LYS H 177 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER H 185 " --> pdb=" O ASN H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 218 Processing helix chain 'H' and resid 270 through 280 removed outlier: 3.562A pdb=" N ASP H 276 " --> pdb=" O GLY H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 311 Processing helix chain 'H' and resid 313 through 327 Processing helix chain 'I' and resid 45 through 51 Processing helix chain 'I' and resid 72 through 86 removed outlier: 3.615A pdb=" N GLU I 86 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 106 Processing helix chain 'I' and resid 122 through 135 Processing helix chain 'I' and resid 152 through 156 Processing helix chain 'I' and resid 166 through 185 removed outlier: 3.527A pdb=" N ARG I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY I 180 " --> pdb=" O ARG I 176 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS I 183 " --> pdb=" O ALA I 179 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER I 185 " --> pdb=" O ASN I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 218 Processing helix chain 'I' and resid 270 through 280 removed outlier: 3.526A pdb=" N ASP I 276 " --> pdb=" O GLY I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 311 Processing helix chain 'I' and resid 313 through 327 Processing sheet with id= A, first strand: chain 'A' and resid 257 through 263 removed outlier: 6.452A pdb=" N ARG A 222 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 221 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 189 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE A 64 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE A 191 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N GLY A 66 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN A 193 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 115 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP A 94 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER A 117 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 195 through 197 Processing sheet with id= C, first strand: chain 'A' and resid 285 through 287 removed outlier: 6.568A pdb=" N TYR A 293 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LYS A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 229 through 233 removed outlier: 3.508A pdb=" N GLY A 229 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU A 233 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 257 through 263 removed outlier: 6.376A pdb=" N ARG B 222 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 221 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 189 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE B 64 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE B 191 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N GLY B 66 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN B 193 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 115 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 195 through 197 Processing sheet with id= G, first strand: chain 'B' and resid 285 through 287 Processing sheet with id= H, first strand: chain 'B' and resid 230 through 233 removed outlier: 6.857A pdb=" N GLU B 233 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 257 through 263 removed outlier: 6.205A pdb=" N ARG C 222 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 221 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU C 189 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE C 64 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE C 191 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N GLY C 66 " --> pdb=" O PHE C 191 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN C 193 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU C 115 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ASP C 94 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER C 117 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 195 through 197 Processing sheet with id= K, first strand: chain 'C' and resid 285 through 287 Processing sheet with id= L, first strand: chain 'C' and resid 229 through 233 removed outlier: 6.706A pdb=" N GLU C 233 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 257 through 263 removed outlier: 6.257A pdb=" N ARG D 222 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL D 221 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU D 189 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE D 64 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE D 191 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N GLY D 66 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN D 193 " --> pdb=" O GLY D 66 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 195 through 197 Processing sheet with id= O, first strand: chain 'D' and resid 285 through 287 removed outlier: 6.850A pdb=" N TYR D 293 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LYS D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 229 through 233 removed outlier: 6.661A pdb=" N GLU D 233 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 257 through 263 removed outlier: 6.280A pdb=" N ARG E 222 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL E 221 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU E 189 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE E 64 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE E 191 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLY E 66 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN E 193 " --> pdb=" O GLY E 66 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 195 through 197 Processing sheet with id= S, first strand: chain 'E' and resid 285 through 287 Processing sheet with id= T, first strand: chain 'E' and resid 229 through 233 removed outlier: 6.736A pdb=" N GLU E 233 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL E 237 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 257 through 263 removed outlier: 6.281A pdb=" N ARG F 222 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL F 221 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU F 189 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE F 64 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE F 191 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N GLY F 66 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN F 193 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU F 115 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP F 94 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER F 117 " --> pdb=" O ASP F 94 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 195 through 197 Processing sheet with id= W, first strand: chain 'F' and resid 285 through 287 Processing sheet with id= X, first strand: chain 'F' and resid 230 through 233 removed outlier: 6.743A pdb=" N GLU F 233 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL F 237 " --> pdb=" O GLU F 233 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 257 through 263 removed outlier: 6.300A pdb=" N ARG G 222 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL G 221 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU G 189 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE G 64 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE G 191 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N GLY G 66 " --> pdb=" O PHE G 191 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN G 193 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU G 115 " --> pdb=" O PHE G 92 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASP G 94 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER G 117 " --> pdb=" O ASP G 94 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 195 through 197 Processing sheet with id= AA, first strand: chain 'G' and resid 285 through 287 removed outlier: 3.563A pdb=" N GLY G 299 " --> pdb=" O TYR G 291 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR G 293 " --> pdb=" O LYS G 297 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LYS G 297 " --> pdb=" O TYR G 293 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 229 through 233 removed outlier: 6.504A pdb=" N GLU G 233 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL G 237 " --> pdb=" O GLU G 233 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 257 through 263 removed outlier: 6.389A pdb=" N ARG H 222 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL H 221 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU H 189 " --> pdb=" O VAL H 62 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE H 64 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE H 191 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N GLY H 66 " --> pdb=" O PHE H 191 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN H 193 " --> pdb=" O GLY H 66 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU H 115 " --> pdb=" O PHE H 92 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASP H 94 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER H 117 " --> pdb=" O ASP H 94 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 195 through 197 Processing sheet with id= AE, first strand: chain 'H' and resid 285 through 287 Processing sheet with id= AF, first strand: chain 'H' and resid 229 through 233 removed outlier: 6.647A pdb=" N GLU H 233 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL H 237 " --> pdb=" O GLU H 233 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 257 through 263 removed outlier: 6.489A pdb=" N ARG I 222 " --> pdb=" O VAL I 247 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL I 221 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU I 189 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE I 64 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE I 191 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLY I 66 " --> pdb=" O PHE I 191 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN I 193 " --> pdb=" O GLY I 66 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU I 115 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASP I 94 " --> pdb=" O LEU I 115 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER I 117 " --> pdb=" O ASP I 94 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 195 through 197 Processing sheet with id= AI, first strand: chain 'I' and resid 285 through 287 removed outlier: 6.467A pdb=" N TYR I 293 " --> pdb=" O LYS I 297 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LYS I 297 " --> pdb=" O TYR I 293 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 229 through 233 removed outlier: 6.836A pdb=" N GLU I 233 " --> pdb=" O VAL I 237 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL I 237 " --> pdb=" O GLU I 233 " (cutoff:3.500A) 990 hydrogen bonds defined for protein. 2898 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 118 hydrogen bonds 236 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 16.89 Time building geometry restraints manager: 32.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.09: 23489 1.09 - 1.34: 7332 1.34 - 1.58: 18727 1.58 - 1.83: 449 1.83 - 2.08: 19 Bond restraints: 50016 Sorted by residual: bond pdb=" C4 AGS I 402 " pdb=" C5 AGS I 402 " ideal model delta sigma weight residual 1.386 1.480 -0.094 1.00e-02 1.00e+04 8.91e+01 bond pdb=" C4 AGS A 402 " pdb=" C5 AGS A 402 " ideal model delta sigma weight residual 1.386 1.480 -0.094 1.00e-02 1.00e+04 8.77e+01 bond pdb=" N3 DT S 12 " pdb=" H3 DT S 12 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" N3 DT U 6 " pdb=" H3 DT U 6 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.18e+01 bond pdb=" N3 DT U 4 " pdb=" H3 DT U 4 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.18e+01 ... (remaining 50011 not shown) Histogram of bond angle deviations from ideal: 85.59 - 95.83: 6 95.83 - 106.07: 1644 106.07 - 116.31: 63762 116.31 - 126.55: 24854 126.55 - 136.80: 608 Bond angle restraints: 90874 Sorted by residual: angle pdb=" C5 AGS G 402 " pdb=" C4 AGS G 402 " pdb=" N3 AGS G 402 " ideal model delta sigma weight residual 126.80 117.60 9.20 7.41e-01 1.82e+00 1.54e+02 angle pdb=" C5 AGS D 402 " pdb=" C4 AGS D 402 " pdb=" N3 AGS D 402 " ideal model delta sigma weight residual 126.80 118.24 8.56 7.41e-01 1.82e+00 1.33e+02 angle pdb=" C5 AGS F 402 " pdb=" C4 AGS F 402 " pdb=" N3 AGS F 402 " ideal model delta sigma weight residual 126.80 118.24 8.56 7.41e-01 1.82e+00 1.33e+02 angle pdb=" C5 AGS H 402 " pdb=" C4 AGS H 402 " pdb=" N3 AGS H 402 " ideal model delta sigma weight residual 126.80 118.27 8.53 7.41e-01 1.82e+00 1.32e+02 angle pdb=" C5 AGS I 402 " pdb=" C4 AGS I 402 " pdb=" N3 AGS I 402 " ideal model delta sigma weight residual 126.80 118.39 8.41 7.41e-01 1.82e+00 1.29e+02 ... (remaining 90869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.89: 20742 31.89 - 63.78: 1841 63.78 - 95.68: 74 95.68 - 127.57: 2 127.57 - 159.46: 10 Dihedral angle restraints: 22669 sinusoidal: 13540 harmonic: 9129 Sorted by residual: dihedral pdb=" CA ASP G 144 " pdb=" C ASP G 144 " pdb=" N SER G 145 " pdb=" CA SER G 145 " ideal model delta harmonic sigma weight residual 180.00 -146.56 -33.44 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA SER D 145 " pdb=" C SER D 145 " pdb=" N VAL D 146 " pdb=" CA VAL D 146 " ideal model delta harmonic sigma weight residual 180.00 148.06 31.94 0 5.00e+00 4.00e-02 4.08e+01 dihedral pdb=" CA ASP F 144 " pdb=" C ASP F 144 " pdb=" N SER F 145 " pdb=" CA SER F 145 " ideal model delta harmonic sigma weight residual -180.00 -149.06 -30.94 0 5.00e+00 4.00e-02 3.83e+01 ... (remaining 22666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2920 0.100 - 0.201: 1004 0.201 - 0.301: 104 0.301 - 0.401: 10 0.401 - 0.501: 1 Chirality restraints: 4039 Sorted by residual: chirality pdb=" C3' DT S 8 " pdb=" C4' DT S 8 " pdb=" O3' DT S 8 " pdb=" C2' DT S 8 " both_signs ideal model delta sigma weight residual False -2.66 -2.16 -0.50 2.00e-01 2.50e+01 6.29e+00 chirality pdb=" CA SER G 145 " pdb=" N SER G 145 " pdb=" C SER G 145 " pdb=" CB SER G 145 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" C2' AGS E 402 " pdb=" C1' AGS E 402 " pdb=" C3' AGS E 402 " pdb=" O2' AGS E 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.29 -0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 4036 not shown) Planarity restraints: 7031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT S 9 " -0.026 2.00e-02 2.50e+03 2.81e-02 2.37e+01 pdb=" N1 DT S 9 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DT S 9 " 0.017 2.00e-02 2.50e+03 pdb=" O2 DT S 9 " 0.026 2.00e-02 2.50e+03 pdb=" N3 DT S 9 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT S 9 " -0.023 2.00e-02 2.50e+03 pdb=" O4 DT S 9 " -0.032 2.00e-02 2.50e+03 pdb=" C5 DT S 9 " -0.008 2.00e-02 2.50e+03 pdb=" C7 DT S 9 " 0.062 2.00e-02 2.50e+03 pdb=" C6 DT S 9 " 0.006 2.00e-02 2.50e+03 pdb=" H3 DT S 9 " -0.007 2.00e-02 2.50e+03 pdb=" H6 DT S 9 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC S 18 " -0.039 2.00e-02 2.50e+03 2.89e-02 2.30e+01 pdb=" N1 DC S 18 " 0.057 2.00e-02 2.50e+03 pdb=" C2 DC S 18 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DC S 18 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DC S 18 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC S 18 " -0.009 2.00e-02 2.50e+03 pdb=" N4 DC S 18 " -0.025 2.00e-02 2.50e+03 pdb=" C5 DC S 18 " 0.018 2.00e-02 2.50e+03 pdb=" C6 DC S 18 " 0.040 2.00e-02 2.50e+03 pdb=" H5 DC S 18 " 0.005 2.00e-02 2.50e+03 pdb=" H6 DC S 18 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT S 8 " 0.005 2.00e-02 2.50e+03 2.69e-02 2.17e+01 pdb=" N1 DT S 8 " -0.063 2.00e-02 2.50e+03 pdb=" C2 DT S 8 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DT S 8 " 0.030 2.00e-02 2.50e+03 pdb=" N3 DT S 8 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT S 8 " -0.005 2.00e-02 2.50e+03 pdb=" O4 DT S 8 " 0.015 2.00e-02 2.50e+03 pdb=" C5 DT S 8 " -0.007 2.00e-02 2.50e+03 pdb=" C7 DT S 8 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT S 8 " -0.023 2.00e-02 2.50e+03 pdb=" H3 DT S 8 " -0.001 2.00e-02 2.50e+03 pdb=" H6 DT S 8 " 0.055 2.00e-02 2.50e+03 ... (remaining 7028 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 1264 2.14 - 2.76: 81661 2.76 - 3.37: 136905 3.37 - 3.99: 181374 3.99 - 4.60: 276088 Nonbonded interactions: 677292 Sorted by model distance: nonbonded pdb="HH11 ARG C 60 " pdb=" HG SER C 220 " model vdw 1.525 2.100 nonbonded pdb="HH11 ARG E 60 " pdb=" HG SER E 220 " model vdw 1.595 2.100 nonbonded pdb="HH11 ARG G 60 " pdb=" HG SER G 220 " model vdw 1.603 2.100 nonbonded pdb=" H GLY B 122 " pdb=" O THR B 150 " model vdw 1.605 1.850 nonbonded pdb="HH11 ARG A 60 " pdb=" HG SER A 220 " model vdw 1.619 2.100 ... (remaining 677287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 333 or resid 401 through 402)) selection = (chain 'B' and (resid 34 through 333 or resid 401 through 402)) selection = (chain 'C' and (resid 34 through 333 or resid 401 through 402)) selection = (chain 'D' and (resid 34 through 333 or resid 401 through 402)) selection = (chain 'E' and (resid 34 through 333 or resid 401 through 402)) selection = (chain 'F' and (resid 34 through 333 or resid 401 through 402)) selection = (chain 'G' and (resid 34 through 333 or resid 401 through 402)) selection = (chain 'H' and (resid 34 through 333 or resid 401 through 402)) selection = chain 'I' } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.480 Construct map_model_manager: 0.530 Extract box with map and model: 5.790 Check model and map are aligned: 0.790 Set scattering table: 0.480 Process input model: 139.700 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 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 : 0.014 0.128 25678 Z= 0.900 Angle : 1.982 23.914 35167 Z= 1.415 Chirality : 0.094 0.501 4039 Planarity : 0.005 0.035 4083 Dihedral : 21.553 159.461 10037 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.77 % Favored : 95.82 % Rotamer: Outliers : 8.61 % Allowed : 9.64 % Favored : 81.75 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.69 (0.12), residues: 2946 helix: -2.04 (0.11), residues: 1258 sheet: 0.25 (0.21), residues: 473 loop : -2.24 (0.14), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 290 HIS 0.008 0.003 HIS F 97 PHE 0.038 0.004 PHE F 217 TYR 0.040 0.004 TYR E 218 ARG 0.014 0.001 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 462 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 ASP cc_start: 0.4624 (OUTLIER) cc_final: 0.4336 (t0) REVERT: B 23 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6419 (tmtm) REVERT: B 308 TRP cc_start: 0.4919 (t60) cc_final: 0.4474 (t60) REVERT: C 8 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.7016 (ttpp) REVERT: C 23 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.7054 (tppp) REVERT: C 158 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6980 (mt-10) REVERT: C 202 MET cc_start: 0.5196 (ptm) cc_final: 0.4939 (ptp) REVERT: C 245 LYS cc_start: 0.8334 (mtpp) cc_final: 0.7997 (mtpp) REVERT: D 20 GLN cc_start: 0.8100 (tt0) cc_final: 0.7390 (tt0) REVERT: D 28 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7846 (mpt180) REVERT: D 105 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7653 (ttm170) REVERT: D 184 GLN cc_start: 0.7189 (mt0) cc_final: 0.6798 (pt0) REVERT: D 241 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8265 (tp30) REVERT: D 285 GLU cc_start: 0.7302 (mp0) cc_final: 0.6851 (mm-30) REVERT: E 8 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7586 (mtmm) REVERT: E 19 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7924 (ttmp) REVERT: E 23 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6547 (tmmt) REVERT: E 40 ILE cc_start: 0.8490 (mm) cc_final: 0.8172 (tt) REVERT: E 86 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6588 (mt-10) REVERT: E 156 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7601 (mm-30) REVERT: E 210 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8018 (p) REVERT: E 216 LYS cc_start: 0.7987 (mttm) cc_final: 0.7628 (mtpt) REVERT: E 245 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8069 (ttmt) REVERT: F 3 ASP cc_start: 0.5138 (OUTLIER) cc_final: 0.4153 (OUTLIER) REVERT: F 4 GLU cc_start: 0.5806 (OUTLIER) cc_final: 0.5370 (mm-30) REVERT: F 6 LYS cc_start: 0.7034 (mtpt) cc_final: 0.6719 (mttp) REVERT: F 23 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6953 (tppt) REVERT: F 38 GLU cc_start: 0.7470 (tt0) cc_final: 0.6953 (mp0) REVERT: F 76 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.7920 (p) REVERT: F 134 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7708 (mtm180) REVERT: F 152 LYS cc_start: 0.7916 (tttm) cc_final: 0.7497 (ttmm) REVERT: F 311 ASP cc_start: 0.5683 (OUTLIER) cc_final: 0.5092 (t0) REVERT: G 63 GLU cc_start: 0.8282 (tt0) cc_final: 0.8049 (tt0) REVERT: G 85 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7836 (mtm-85) REVERT: G 105 ARG cc_start: 0.7842 (ttm-80) cc_final: 0.7407 (ttp80) REVERT: G 158 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7380 (tp30) REVERT: G 240 SER cc_start: 0.8421 (m) cc_final: 0.8207 (p) REVERT: G 245 LYS cc_start: 0.8067 (mttp) cc_final: 0.7583 (mtpp) REVERT: G 315 THR cc_start: 0.4769 (OUTLIER) cc_final: 0.4131 (t) REVERT: G 327 LEU cc_start: 0.7215 (mt) cc_final: 0.6979 (mt) REVERT: H 85 ARG cc_start: 0.7740 (mtt90) cc_final: 0.7516 (mtm-85) REVERT: H 105 ARG cc_start: 0.7387 (ttm-80) cc_final: 0.7170 (ttp80) REVERT: H 210 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7867 (p) REVERT: I 150 THR cc_start: 0.5848 (OUTLIER) cc_final: 0.5578 (t) REVERT: I 172 SER cc_start: 0.0527 (OUTLIER) cc_final: 0.0073 (p) REVERT: I 282 LYS cc_start: 0.4710 (mmtt) cc_final: 0.3672 (ttpp) outliers start: 201 outliers final: 33 residues processed: 616 average time/residue: 2.4973 time to fit residues: 1766.5393 Evaluate side-chains 325 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 272 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain F residue 3 ASP Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 322 LYS Chi-restraints excluded: chain G residue 85 ARG Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain H residue 6 LYS Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 185 SER Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 238 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 177 optimal weight: 0.8980 chunk 276 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 257 GLN B 20 GLN B 124 GLN B 257 GLN D 16 GLN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN F 184 GLN I 269 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25678 Z= 0.205 Angle : 0.630 5.201 35167 Z= 0.355 Chirality : 0.042 0.156 4039 Planarity : 0.004 0.042 4083 Dihedral : 20.803 157.807 4756 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.87 % Favored : 97.90 % Rotamer: Outliers : 4.33 % Allowed : 18.89 % Favored : 76.78 % 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: -0.82 (0.14), residues: 2946 helix: 0.23 (0.14), residues: 1284 sheet: 0.62 (0.21), residues: 504 loop : -1.96 (0.15), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 290 HIS 0.004 0.001 HIS A 97 PHE 0.018 0.001 PHE C 203 TYR 0.009 0.002 TYR G 65 ARG 0.004 0.001 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 302 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 MET cc_start: 0.6732 (ttp) cc_final: 0.6501 (ttt) REVERT: B 23 LYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6550 (tmtm) REVERT: B 308 TRP cc_start: 0.5221 (t60) cc_final: 0.4676 (t60) REVERT: B 326 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7555 (mp) REVERT: C 158 GLU cc_start: 0.7330 (mt-10) cc_final: 0.7100 (mt-10) REVERT: C 184 GLN cc_start: 0.7109 (mt0) cc_final: 0.6651 (pt0) REVERT: C 245 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7624 (tmtm) REVERT: D 20 GLN cc_start: 0.7837 (tt0) cc_final: 0.7177 (tt0) REVERT: D 105 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7656 (ttm170) REVERT: D 184 GLN cc_start: 0.7140 (mt0) cc_final: 0.6922 (mp10) REVERT: E 19 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7784 (ttmt) REVERT: E 23 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6952 (mmmt) REVERT: E 40 ILE cc_start: 0.8253 (mm) cc_final: 0.8000 (tt) REVERT: E 86 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6607 (mt-10) REVERT: E 106 LYS cc_start: 0.8720 (mttt) cc_final: 0.8502 (mtmt) REVERT: E 156 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7597 (mm-30) REVERT: E 216 LYS cc_start: 0.7554 (mttm) cc_final: 0.7269 (mtpt) REVERT: E 259 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: E 280 LYS cc_start: 0.8349 (ttpp) cc_final: 0.7971 (ptmm) REVERT: E 326 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7436 (mt) REVERT: F 6 LYS cc_start: 0.7081 (mtpt) cc_final: 0.6785 (mttp) REVERT: F 23 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6975 (tppt) REVERT: F 38 GLU cc_start: 0.7254 (tt0) cc_final: 0.6510 (mp0) REVERT: F 152 LYS cc_start: 0.8016 (tttm) cc_final: 0.7630 (ttmm) REVERT: F 216 LYS cc_start: 0.7613 (mttm) cc_final: 0.7401 (mtmt) REVERT: F 241 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7344 (tp30) REVERT: F 308 TRP cc_start: 0.6224 (t60) cc_final: 0.5854 (t60) REVERT: F 311 ASP cc_start: 0.5699 (OUTLIER) cc_final: 0.4879 (t0) REVERT: G 105 ARG cc_start: 0.7744 (ttm-80) cc_final: 0.7225 (ttp80) REVERT: G 158 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7304 (tp30) REVERT: G 240 SER cc_start: 0.8562 (m) cc_final: 0.8317 (p) REVERT: G 245 LYS cc_start: 0.7654 (mttp) cc_final: 0.7151 (mmmt) REVERT: G 327 LEU cc_start: 0.7121 (mt) cc_final: 0.6910 (mt) REVERT: H 38 GLU cc_start: 0.5709 (OUTLIER) cc_final: 0.5238 (tt0) REVERT: H 210 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.8049 (p) REVERT: I 135 SER cc_start: 0.4499 (p) cc_final: 0.4208 (m) REVERT: I 154 GLU cc_start: 0.4853 (OUTLIER) cc_final: 0.3960 (tm-30) REVERT: I 172 SER cc_start: 0.1129 (OUTLIER) cc_final: 0.0571 (p) outliers start: 101 outliers final: 41 residues processed: 376 average time/residue: 2.2709 time to fit residues: 995.0307 Evaluate side-chains 307 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 253 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 296 GLU Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 229 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 276 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 274 optimal weight: 40.0000 chunk 94 optimal weight: 9.9990 chunk 221 optimal weight: 0.8980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN D 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25678 Z= 0.238 Angle : 0.580 6.271 35167 Z= 0.321 Chirality : 0.044 0.153 4039 Planarity : 0.004 0.047 4083 Dihedral : 20.207 157.871 4688 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 3.51 % Allowed : 20.18 % Favored : 76.31 % 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: -0.20 (0.15), residues: 2946 helix: 1.06 (0.14), residues: 1283 sheet: 0.66 (0.21), residues: 494 loop : -1.89 (0.15), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 290 HIS 0.004 0.001 HIS E 97 PHE 0.012 0.002 PHE C 203 TYR 0.017 0.002 TYR G 291 ARG 0.007 0.001 ARG F 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 255 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.5982 (mpp) cc_final: 0.5703 (mpp) REVERT: A 194 GLN cc_start: 0.6560 (OUTLIER) cc_final: 0.5702 (mm110) REVERT: B 23 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6585 (tmtm) REVERT: B 308 TRP cc_start: 0.5365 (t60) cc_final: 0.4649 (t60) REVERT: B 326 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7546 (mp) REVERT: C 158 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7038 (mt-10) REVERT: C 172 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.8289 (m) REVERT: C 184 GLN cc_start: 0.7098 (mt0) cc_final: 0.6760 (pt0) REVERT: C 241 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7390 (mm-30) REVERT: C 245 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7662 (tmtm) REVERT: D 20 GLN cc_start: 0.7844 (tt0) cc_final: 0.7243 (tt0) REVERT: D 105 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7703 (ttm170) REVERT: D 184 GLN cc_start: 0.7252 (mt0) cc_final: 0.7048 (mp10) REVERT: D 302 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7244 (ttpm) REVERT: E 19 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7688 (ttpp) REVERT: E 40 ILE cc_start: 0.8233 (mm) cc_final: 0.7921 (tt) REVERT: E 86 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6745 (mt-10) REVERT: E 156 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7604 (mm-30) REVERT: E 216 LYS cc_start: 0.7735 (mttm) cc_final: 0.7521 (mtpt) REVERT: E 259 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: E 310 LYS cc_start: 0.7752 (mtpt) cc_final: 0.7522 (mtpp) REVERT: E 326 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7299 (mt) REVERT: F 6 LYS cc_start: 0.6974 (mtpt) cc_final: 0.6696 (mttp) REVERT: F 152 LYS cc_start: 0.8102 (tttm) cc_final: 0.7794 (ttpm) REVERT: F 216 LYS cc_start: 0.7841 (mttm) cc_final: 0.7588 (mtmt) REVERT: F 311 ASP cc_start: 0.5757 (OUTLIER) cc_final: 0.5133 (t0) REVERT: G 105 ARG cc_start: 0.7798 (ttm-80) cc_final: 0.7297 (ttp80) REVERT: G 158 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7390 (tp30) REVERT: G 240 SER cc_start: 0.8726 (m) cc_final: 0.8454 (p) REVERT: G 245 LYS cc_start: 0.7710 (mttp) cc_final: 0.7233 (mtpp) REVERT: G 315 THR cc_start: 0.4707 (OUTLIER) cc_final: 0.4275 (m) REVERT: H 38 GLU cc_start: 0.5510 (OUTLIER) cc_final: 0.4996 (tt0) REVERT: H 210 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8275 (p) REVERT: I 135 SER cc_start: 0.4647 (p) cc_final: 0.4324 (m) REVERT: I 172 SER cc_start: 0.1455 (OUTLIER) cc_final: 0.0879 (p) REVERT: I 296 GLU cc_start: 0.0974 (OUTLIER) cc_final: 0.0628 (pt0) outliers start: 82 outliers final: 38 residues processed: 316 average time/residue: 2.2955 time to fit residues: 848.3282 Evaluate side-chains 286 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 233 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 296 GLU Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 chunk 293 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN D 16 GLN G 184 GLN I 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 25678 Z= 0.381 Angle : 0.639 8.766 35167 Z= 0.348 Chirality : 0.047 0.156 4039 Planarity : 0.005 0.061 4083 Dihedral : 20.267 171.088 4673 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.55 % Favored : 97.32 % Rotamer: Outliers : 4.28 % Allowed : 19.88 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.37 (0.14), residues: 2946 helix: 0.89 (0.14), residues: 1283 sheet: 0.72 (0.22), residues: 446 loop : -1.91 (0.14), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 290 HIS 0.008 0.002 HIS E 97 PHE 0.020 0.002 PHE F 217 TYR 0.018 0.002 TYR G 291 ARG 0.007 0.001 ARG F 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 243 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6311 (mpp) cc_final: 0.5921 (mtt) REVERT: A 194 GLN cc_start: 0.6614 (OUTLIER) cc_final: 0.5755 (mm110) REVERT: B 23 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6589 (tmtm) REVERT: B 308 TRP cc_start: 0.5391 (t60) cc_final: 0.4752 (t60) REVERT: B 326 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7438 (mp) REVERT: C 86 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: C 158 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7237 (mt-10) REVERT: C 172 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8432 (m) REVERT: C 184 GLN cc_start: 0.7172 (mt0) cc_final: 0.6640 (pt0) REVERT: C 241 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7486 (mm-30) REVERT: C 245 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7790 (mtpp) REVERT: D 20 GLN cc_start: 0.7949 (tt0) cc_final: 0.7211 (tt0) REVERT: D 105 ARG cc_start: 0.8050 (ttm-80) cc_final: 0.7795 (ttm170) REVERT: D 184 GLN cc_start: 0.7124 (mt0) cc_final: 0.6894 (mp10) REVERT: D 259 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: D 302 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7199 (ttpm) REVERT: E 19 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7675 (ttpp) REVERT: E 40 ILE cc_start: 0.8426 (mm) cc_final: 0.8016 (tp) REVERT: E 156 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7596 (mm-30) REVERT: E 184 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.7093 (mt0) REVERT: E 326 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7256 (mt) REVERT: F 6 LYS cc_start: 0.7143 (mtpt) cc_final: 0.6912 (mttp) REVERT: F 152 LYS cc_start: 0.8172 (tttm) cc_final: 0.7865 (ttpm) REVERT: F 311 ASP cc_start: 0.5964 (OUTLIER) cc_final: 0.5377 (t0) REVERT: G 105 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7369 (ttp80) REVERT: G 158 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7446 (tp30) REVERT: G 240 SER cc_start: 0.8750 (m) cc_final: 0.8482 (p) REVERT: G 245 LYS cc_start: 0.7961 (mttp) cc_final: 0.7465 (mtpp) REVERT: I 135 SER cc_start: 0.4502 (p) cc_final: 0.4204 (m) REVERT: I 154 GLU cc_start: 0.5254 (OUTLIER) cc_final: 0.4824 (tt0) REVERT: I 172 SER cc_start: 0.1678 (OUTLIER) cc_final: 0.1076 (p) REVERT: I 296 GLU cc_start: 0.0968 (OUTLIER) cc_final: 0.0528 (pt0) outliers start: 100 outliers final: 52 residues processed: 318 average time/residue: 2.2243 time to fit residues: 828.4997 Evaluate side-chains 298 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 231 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain D residue 322 LYS Chi-restraints excluded: chain D residue 332 ASN Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 3 ASP Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 224 ASP Chi-restraints excluded: chain I residue 232 LYS Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 296 GLU Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 218 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 203 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 236 ASN G 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25678 Z= 0.176 Angle : 0.524 4.703 35167 Z= 0.294 Chirality : 0.042 0.144 4039 Planarity : 0.004 0.046 4083 Dihedral : 20.006 164.896 4669 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.93 % Favored : 97.96 % Rotamer: Outliers : 3.13 % Allowed : 20.91 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.06 (0.15), residues: 2946 helix: 1.35 (0.15), residues: 1299 sheet: 0.83 (0.22), residues: 450 loop : -1.81 (0.15), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 308 HIS 0.003 0.001 HIS E 97 PHE 0.012 0.001 PHE E 203 TYR 0.009 0.001 TYR E 65 ARG 0.005 0.000 ARG H 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 245 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6245 (mpp) cc_final: 0.5951 (mtt) REVERT: A 321 LYS cc_start: 0.6104 (OUTLIER) cc_final: 0.5844 (ttpp) REVERT: B 23 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6600 (tmtm) REVERT: B 308 TRP cc_start: 0.5379 (t60) cc_final: 0.4691 (t60) REVERT: B 326 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7354 (mp) REVERT: C 86 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: C 172 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8250 (m) REVERT: C 184 GLN cc_start: 0.7162 (mt0) cc_final: 0.6725 (pt0) REVERT: C 245 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7723 (mtpp) REVERT: C 309 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6320 (tt) REVERT: D 19 LYS cc_start: 0.7269 (tppt) cc_final: 0.6419 (tmtt) REVERT: D 20 GLN cc_start: 0.7950 (tt0) cc_final: 0.7163 (tt0) REVERT: D 68 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7608 (pm20) REVERT: D 105 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7764 (ttm170) REVERT: D 184 GLN cc_start: 0.7099 (mt0) cc_final: 0.6865 (mp10) REVERT: D 302 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7217 (ttpm) REVERT: E 19 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7669 (ttpp) REVERT: E 40 ILE cc_start: 0.8351 (mm) cc_final: 0.7950 (tp) REVERT: E 110 ASP cc_start: 0.8538 (t0) cc_final: 0.8059 (t70) REVERT: E 156 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7596 (mm-30) REVERT: E 184 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6983 (mt0) REVERT: F 6 LYS cc_start: 0.7079 (mtpt) cc_final: 0.6771 (mttp) REVERT: F 19 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7201 (tmtp) REVERT: F 152 LYS cc_start: 0.8152 (tttm) cc_final: 0.7862 (ttpm) REVERT: F 256 LYS cc_start: 0.8286 (mttt) cc_final: 0.8004 (mttp) REVERT: F 311 ASP cc_start: 0.5915 (OUTLIER) cc_final: 0.5434 (t0) REVERT: G 35 MET cc_start: 0.8512 (mtt) cc_final: 0.8243 (mtt) REVERT: G 68 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7158 (pp20) REVERT: G 105 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7374 (ttp80) REVERT: G 158 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7438 (tp30) REVERT: G 240 SER cc_start: 0.8735 (m) cc_final: 0.8489 (p) REVERT: G 245 LYS cc_start: 0.7767 (mttp) cc_final: 0.7222 (mtpp) REVERT: G 315 THR cc_start: 0.4901 (OUTLIER) cc_final: 0.4640 (m) REVERT: I 135 SER cc_start: 0.4479 (p) cc_final: 0.4204 (m) REVERT: I 296 GLU cc_start: 0.1095 (OUTLIER) cc_final: 0.0674 (pt0) outliers start: 73 outliers final: 38 residues processed: 295 average time/residue: 2.1892 time to fit residues: 757.2257 Evaluate side-chains 287 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 234 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 302 LYS Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 296 GLU Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 3.9990 chunk 264 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 294 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN C 236 ASN F 184 GLN G 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25678 Z= 0.251 Angle : 0.545 6.101 35167 Z= 0.301 Chirality : 0.043 0.143 4039 Planarity : 0.004 0.048 4083 Dihedral : 19.900 161.120 4665 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.38 % Favored : 97.52 % Rotamer: Outliers : 3.86 % Allowed : 20.87 % Favored : 75.28 % 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: 0.22 (0.15), residues: 2946 helix: 1.63 (0.15), residues: 1235 sheet: 0.68 (0.21), residues: 498 loop : -1.74 (0.15), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 290 HIS 0.004 0.001 HIS E 97 PHE 0.018 0.001 PHE E 203 TYR 0.020 0.001 TYR I 218 ARG 0.003 0.000 ARG E 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 252 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6353 (mpp) cc_final: 0.6073 (mtt) REVERT: A 194 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.5259 (mm110) REVERT: A 321 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.5813 (ttpp) REVERT: B 23 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6599 (tmtm) REVERT: B 308 TRP cc_start: 0.5407 (t60) cc_final: 0.4749 (t60) REVERT: B 326 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7298 (mp) REVERT: C 86 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: C 172 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8256 (m) REVERT: C 184 GLN cc_start: 0.7129 (mt0) cc_final: 0.6696 (pt0) REVERT: C 241 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: C 245 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7737 (mtpp) REVERT: C 309 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6238 (tt) REVERT: D 20 GLN cc_start: 0.7977 (tt0) cc_final: 0.7291 (tt0) REVERT: D 68 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: D 105 ARG cc_start: 0.8068 (ttm-80) cc_final: 0.7791 (ttm170) REVERT: D 184 GLN cc_start: 0.7049 (mt0) cc_final: 0.6821 (mp10) REVERT: E 19 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7728 (ttpp) REVERT: E 40 ILE cc_start: 0.8398 (mm) cc_final: 0.8001 (tp) REVERT: E 110 ASP cc_start: 0.8549 (t0) cc_final: 0.8078 (t70) REVERT: E 156 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7681 (mm-30) REVERT: E 326 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7114 (mt) REVERT: F 6 LYS cc_start: 0.7149 (mtpt) cc_final: 0.6855 (mttp) REVERT: F 19 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7183 (tmtp) REVERT: F 152 LYS cc_start: 0.8144 (tttm) cc_final: 0.7857 (ttpm) REVERT: F 256 LYS cc_start: 0.8297 (mttt) cc_final: 0.7985 (mttp) REVERT: F 311 ASP cc_start: 0.6079 (OUTLIER) cc_final: 0.5755 (OUTLIER) REVERT: G 35 MET cc_start: 0.8518 (mtt) cc_final: 0.8193 (mtt) REVERT: G 68 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7216 (pp20) REVERT: G 86 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: G 105 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7358 (ttp80) REVERT: G 158 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7461 (tp30) REVERT: G 240 SER cc_start: 0.8742 (m) cc_final: 0.8491 (p) REVERT: G 315 THR cc_start: 0.4998 (OUTLIER) cc_final: 0.4720 (m) REVERT: I 130 ASP cc_start: 0.3497 (OUTLIER) cc_final: 0.3295 (m-30) REVERT: I 135 SER cc_start: 0.4459 (p) cc_final: 0.4195 (m) REVERT: I 172 SER cc_start: 0.1432 (OUTLIER) cc_final: 0.0910 (p) REVERT: I 175 MET cc_start: 0.1734 (mmm) cc_final: 0.1289 (mmm) REVERT: I 296 GLU cc_start: 0.0956 (OUTLIER) cc_final: 0.0529 (pt0) outliers start: 90 outliers final: 49 residues processed: 317 average time/residue: 2.1536 time to fit residues: 803.3835 Evaluate side-chains 304 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 237 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 232 LYS Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 296 GLU Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 214 optimal weight: 0.4980 chunk 166 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 164 optimal weight: 0.3980 chunk 293 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN F 236 ASN G 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25678 Z= 0.183 Angle : 0.511 5.904 35167 Z= 0.285 Chirality : 0.042 0.142 4039 Planarity : 0.003 0.042 4083 Dihedral : 19.788 160.760 4665 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.80 % Favored : 98.10 % Rotamer: Outliers : 3.00 % Allowed : 21.89 % Favored : 75.11 % 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: 0.44 (0.15), residues: 2946 helix: 1.84 (0.15), residues: 1235 sheet: 0.76 (0.21), residues: 498 loop : -1.63 (0.15), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 290 HIS 0.003 0.001 HIS E 97 PHE 0.018 0.001 PHE E 203 TYR 0.008 0.001 TYR E 65 ARG 0.002 0.000 ARG F 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 252 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6326 (mpp) cc_final: 0.6037 (mtt) REVERT: A 194 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6577 (mm-40) REVERT: B 23 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6659 (tmtm) REVERT: B 326 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7240 (mp) REVERT: C 86 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: C 172 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8208 (m) REVERT: C 184 GLN cc_start: 0.7099 (mt0) cc_final: 0.6682 (pt0) REVERT: C 241 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: C 245 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7695 (mtpp) REVERT: C 309 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6317 (tt) REVERT: D 20 GLN cc_start: 0.7977 (tt0) cc_final: 0.7250 (tt0) REVERT: D 105 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7786 (ttm170) REVERT: D 285 GLU cc_start: 0.7566 (mp0) cc_final: 0.6891 (mm-30) REVERT: E 19 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7670 (ttpp) REVERT: E 40 ILE cc_start: 0.8342 (mm) cc_final: 0.8052 (tt) REVERT: E 110 ASP cc_start: 0.8516 (t0) cc_final: 0.8061 (t70) REVERT: E 156 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7680 (mm-30) REVERT: E 326 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7103 (mt) REVERT: F 6 LYS cc_start: 0.7154 (mtpt) cc_final: 0.6864 (mttp) REVERT: F 152 LYS cc_start: 0.8155 (tttm) cc_final: 0.7885 (ttpm) REVERT: F 256 LYS cc_start: 0.8322 (mttt) cc_final: 0.8017 (mttp) REVERT: F 311 ASP cc_start: 0.6142 (OUTLIER) cc_final: 0.5875 (t0) REVERT: G 35 MET cc_start: 0.8519 (mtt) cc_final: 0.8204 (mtt) REVERT: G 86 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: G 105 ARG cc_start: 0.7852 (ttm-80) cc_final: 0.7328 (ttp80) REVERT: G 158 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7492 (tp30) REVERT: G 240 SER cc_start: 0.8730 (m) cc_final: 0.8479 (p) REVERT: G 315 THR cc_start: 0.4919 (OUTLIER) cc_final: 0.4642 (m) REVERT: I 135 SER cc_start: 0.4479 (p) cc_final: 0.4206 (m) REVERT: I 172 SER cc_start: 0.1367 (OUTLIER) cc_final: 0.0912 (p) REVERT: I 175 MET cc_start: 0.1945 (mmm) cc_final: 0.1499 (mmm) REVERT: I 296 GLU cc_start: 0.0920 (OUTLIER) cc_final: 0.0551 (pt0) outliers start: 70 outliers final: 42 residues processed: 303 average time/residue: 2.1888 time to fit residues: 779.9187 Evaluate side-chains 292 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 236 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 296 GLU Chi-restraints excluded: chain I residue 306 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN F 236 ASN G 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25678 Z= 0.260 Angle : 0.548 7.282 35167 Z= 0.301 Chirality : 0.043 0.144 4039 Planarity : 0.004 0.048 4083 Dihedral : 19.765 161.152 4658 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.31 % Favored : 97.59 % Rotamer: Outliers : 3.43 % Allowed : 21.98 % Favored : 74.59 % 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: 0.36 (0.15), residues: 2946 helix: 1.75 (0.15), residues: 1235 sheet: 0.71 (0.21), residues: 498 loop : -1.64 (0.15), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 308 HIS 0.005 0.001 HIS E 97 PHE 0.019 0.001 PHE E 203 TYR 0.010 0.001 TYR A 271 ARG 0.003 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 244 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6416 (mpp) cc_final: 0.6100 (mtt) REVERT: A 194 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6580 (mm-40) REVERT: A 321 LYS cc_start: 0.6221 (OUTLIER) cc_final: 0.5952 (ttpp) REVERT: B 23 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6628 (ttpp) REVERT: B 40 ILE cc_start: 0.8001 (mt) cc_final: 0.7797 (pt) REVERT: B 326 LEU cc_start: 0.7642 (mt) cc_final: 0.7249 (mp) REVERT: C 86 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: C 172 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8245 (m) REVERT: C 184 GLN cc_start: 0.7129 (mt0) cc_final: 0.6707 (pt0) REVERT: C 241 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7439 (mm-30) REVERT: C 245 LYS cc_start: 0.8143 (mtpp) cc_final: 0.7735 (mtpp) REVERT: C 309 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6247 (tt) REVERT: D 20 GLN cc_start: 0.7986 (tt0) cc_final: 0.7304 (tt0) REVERT: D 105 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7815 (ttm170) REVERT: D 285 GLU cc_start: 0.7589 (mp0) cc_final: 0.6927 (mm-30) REVERT: E 19 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7691 (ttpp) REVERT: E 40 ILE cc_start: 0.8402 (mm) cc_final: 0.8102 (tt) REVERT: E 110 ASP cc_start: 0.8527 (t0) cc_final: 0.8101 (t70) REVERT: E 156 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7676 (mm-30) REVERT: E 282 LYS cc_start: 0.7796 (mmtt) cc_final: 0.7231 (mtmm) REVERT: E 326 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7090 (mt) REVERT: F 6 LYS cc_start: 0.7167 (mtpt) cc_final: 0.6898 (mttp) REVERT: F 152 LYS cc_start: 0.8143 (tttm) cc_final: 0.7859 (ttpm) REVERT: F 256 LYS cc_start: 0.8293 (mttt) cc_final: 0.7974 (mttp) REVERT: F 311 ASP cc_start: 0.6104 (OUTLIER) cc_final: 0.5878 (t0) REVERT: G 35 MET cc_start: 0.8517 (mtt) cc_final: 0.8223 (mtt) REVERT: G 68 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7144 (pp20) REVERT: G 86 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: G 105 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7338 (ttp80) REVERT: G 158 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7445 (tp30) REVERT: G 240 SER cc_start: 0.8742 (m) cc_final: 0.8484 (p) REVERT: G 315 THR cc_start: 0.4900 (OUTLIER) cc_final: 0.4622 (m) REVERT: H 68 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6779 (pp20) REVERT: H 184 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7355 (mt0) REVERT: I 135 SER cc_start: 0.4368 (p) cc_final: 0.4164 (m) REVERT: I 172 SER cc_start: 0.1404 (OUTLIER) cc_final: 0.0924 (p) REVERT: I 232 LYS cc_start: 0.4833 (OUTLIER) cc_final: 0.4598 (ttpt) REVERT: I 296 GLU cc_start: 0.0939 (OUTLIER) cc_final: 0.0545 (pt0) outliers start: 80 outliers final: 50 residues processed: 305 average time/residue: 2.2432 time to fit residues: 804.6191 Evaluate side-chains 303 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 235 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 232 LYS Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 296 GLU Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 20.0000 chunk 280 optimal weight: 10.0000 chunk 256 optimal weight: 0.7980 chunk 273 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 chunk 258 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN F 236 ASN G 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25678 Z= 0.243 Angle : 0.534 6.603 35167 Z= 0.296 Chirality : 0.043 0.146 4039 Planarity : 0.004 0.043 4083 Dihedral : 19.704 160.626 4654 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.14 % Favored : 97.76 % Rotamer: Outliers : 3.17 % Allowed : 22.37 % Favored : 74.46 % 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: 0.40 (0.15), residues: 2946 helix: 1.77 (0.15), residues: 1234 sheet: 0.71 (0.21), residues: 498 loop : -1.60 (0.15), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 308 HIS 0.004 0.001 HIS A 97 PHE 0.019 0.001 PHE E 203 TYR 0.011 0.001 TYR I 271 ARG 0.005 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 246 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6448 (mpp) cc_final: 0.6154 (mtt) REVERT: A 194 GLN cc_start: 0.6860 (OUTLIER) cc_final: 0.6652 (mm-40) REVERT: A 321 LYS cc_start: 0.6177 (OUTLIER) cc_final: 0.5923 (ttpp) REVERT: B 23 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6616 (ttpp) REVERT: B 326 LEU cc_start: 0.7643 (mt) cc_final: 0.7235 (mp) REVERT: C 86 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: C 172 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8234 (m) REVERT: C 184 GLN cc_start: 0.7033 (mt0) cc_final: 0.6721 (pt0) REVERT: C 245 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7705 (mtpp) REVERT: C 309 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6246 (tt) REVERT: D 20 GLN cc_start: 0.7995 (tt0) cc_final: 0.7288 (tt0) REVERT: D 105 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7812 (ttm170) REVERT: D 285 GLU cc_start: 0.7583 (mp0) cc_final: 0.6939 (mm-30) REVERT: E 19 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7685 (ttpp) REVERT: E 40 ILE cc_start: 0.8392 (mm) cc_final: 0.8131 (tt) REVERT: E 110 ASP cc_start: 0.8514 (t0) cc_final: 0.8091 (t70) REVERT: E 156 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7651 (mm-30) REVERT: E 282 LYS cc_start: 0.7797 (mmtt) cc_final: 0.7219 (mtmm) REVERT: E 326 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7065 (mt) REVERT: F 6 LYS cc_start: 0.7138 (mtpt) cc_final: 0.6875 (mttp) REVERT: F 152 LYS cc_start: 0.8166 (tttm) cc_final: 0.7869 (ttpm) REVERT: F 256 LYS cc_start: 0.8323 (mttt) cc_final: 0.8044 (mttp) REVERT: G 25 SER cc_start: 0.8148 (OUTLIER) cc_final: 0.7817 (t) REVERT: G 35 MET cc_start: 0.8524 (mtt) cc_final: 0.8247 (mtt) REVERT: G 68 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7143 (pp20) REVERT: G 86 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: G 105 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7345 (ttp80) REVERT: G 158 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7478 (tp30) REVERT: G 240 SER cc_start: 0.8733 (m) cc_final: 0.8476 (p) REVERT: G 315 THR cc_start: 0.4967 (OUTLIER) cc_final: 0.4679 (m) REVERT: I 135 SER cc_start: 0.4371 (p) cc_final: 0.4165 (m) REVERT: I 172 SER cc_start: 0.1388 (OUTLIER) cc_final: 0.0943 (p) REVERT: I 175 MET cc_start: 0.1754 (mmm) cc_final: 0.1389 (mmm) REVERT: I 232 LYS cc_start: 0.4809 (OUTLIER) cc_final: 0.4598 (ttpt) REVERT: I 296 GLU cc_start: 0.0925 (OUTLIER) cc_final: 0.0545 (pt0) outliers start: 74 outliers final: 47 residues processed: 300 average time/residue: 2.2762 time to fit residues: 805.2401 Evaluate side-chains 300 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 238 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 224 ASP Chi-restraints excluded: chain I residue 232 LYS Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 296 GLU Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 2.9990 chunk 288 optimal weight: 20.0000 chunk 176 optimal weight: 2.9990 chunk 136 optimal weight: 0.0570 chunk 200 optimal weight: 10.0000 chunk 302 optimal weight: 9.9990 chunk 278 optimal weight: 8.9990 chunk 241 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN F 236 ASN G 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25678 Z= 0.241 Angle : 0.537 6.283 35167 Z= 0.297 Chirality : 0.043 0.146 4039 Planarity : 0.004 0.058 4083 Dihedral : 19.668 160.925 4651 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 2.87 % Allowed : 22.88 % Favored : 74.25 % 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: 0.42 (0.15), residues: 2946 helix: 1.80 (0.15), residues: 1234 sheet: 0.69 (0.21), residues: 494 loop : -1.59 (0.15), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 308 HIS 0.004 0.001 HIS E 97 PHE 0.021 0.001 PHE E 203 TYR 0.010 0.001 TYR A 271 ARG 0.009 0.000 ARG I 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 243 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.6435 (mpp) cc_final: 0.6193 (mtt) REVERT: A 194 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6698 (mm-40) REVERT: A 321 LYS cc_start: 0.6238 (OUTLIER) cc_final: 0.6013 (ttpp) REVERT: B 23 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6656 (ttpp) REVERT: B 326 LEU cc_start: 0.7629 (mt) cc_final: 0.7217 (mp) REVERT: C 86 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: C 172 SER cc_start: 0.8665 (OUTLIER) cc_final: 0.8239 (m) REVERT: C 184 GLN cc_start: 0.7102 (mt0) cc_final: 0.6669 (pt0) REVERT: C 245 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7713 (mtpp) REVERT: C 309 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6244 (tt) REVERT: D 20 GLN cc_start: 0.7969 (tt0) cc_final: 0.7292 (tt0) REVERT: D 105 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.7811 (ttm170) REVERT: D 285 GLU cc_start: 0.7507 (mp0) cc_final: 0.6900 (mm-30) REVERT: E 19 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7678 (ttpp) REVERT: E 40 ILE cc_start: 0.8371 (mm) cc_final: 0.8111 (tt) REVERT: E 110 ASP cc_start: 0.8508 (t0) cc_final: 0.8070 (t70) REVERT: E 156 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7643 (mm-30) REVERT: E 282 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7221 (mtmm) REVERT: E 326 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7047 (mt) REVERT: F 6 LYS cc_start: 0.7142 (mtpt) cc_final: 0.6911 (mttp) REVERT: F 152 LYS cc_start: 0.8170 (tttm) cc_final: 0.7870 (ttpm) REVERT: F 256 LYS cc_start: 0.8314 (mttt) cc_final: 0.8037 (mttp) REVERT: G 25 SER cc_start: 0.8144 (OUTLIER) cc_final: 0.7826 (t) REVERT: G 35 MET cc_start: 0.8525 (mtt) cc_final: 0.8250 (mtt) REVERT: G 68 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7144 (pp20) REVERT: G 86 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: G 105 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7346 (ttp80) REVERT: G 158 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7479 (tp30) REVERT: G 240 SER cc_start: 0.8737 (m) cc_final: 0.8475 (p) REVERT: G 315 THR cc_start: 0.4982 (OUTLIER) cc_final: 0.4692 (m) REVERT: I 105 ARG cc_start: 0.6678 (mtm110) cc_final: 0.6473 (mtp180) REVERT: I 135 SER cc_start: 0.4365 (p) cc_final: 0.4159 (m) REVERT: I 172 SER cc_start: 0.1382 (OUTLIER) cc_final: 0.0945 (p) REVERT: I 175 MET cc_start: 0.1706 (mmm) cc_final: 0.1302 (mmm) REVERT: I 232 LYS cc_start: 0.4803 (OUTLIER) cc_final: 0.4562 (ttpt) REVERT: I 296 GLU cc_start: 0.1162 (OUTLIER) cc_final: 0.0797 (pt0) outliers start: 67 outliers final: 47 residues processed: 294 average time/residue: 2.3154 time to fit residues: 798.7861 Evaluate side-chains 301 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 239 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 232 LYS Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 292 SER Chi-restraints excluded: chain I residue 296 GLU Chi-restraints excluded: chain I residue 306 THR Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 2.9990 chunk 256 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 241 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 248 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 44 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN G 184 GLN I 257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.208261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.152671 restraints weight = 71365.318| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.73 r_work: 0.3133 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25678 Z= 0.144 Angle : 0.491 5.312 35167 Z= 0.275 Chirality : 0.041 0.142 4039 Planarity : 0.003 0.063 4083 Dihedral : 19.490 159.661 4651 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.06 % Allowed : 23.61 % Favored : 74.34 % 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: 0.74 (0.15), residues: 2946 helix: 2.16 (0.15), residues: 1227 sheet: 0.80 (0.21), residues: 494 loop : -1.47 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 308 HIS 0.002 0.001 HIS A 163 PHE 0.020 0.001 PHE E 203 TYR 0.008 0.001 TYR A 271 ARG 0.011 0.000 ARG I 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14512.58 seconds wall clock time: 250 minutes 9.61 seconds (15009.61 seconds total)