Starting phenix.real_space_refine on Wed Feb 21 19:12:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy6_22522/02_2024/7jy6_22522_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy6_22522/02_2024/7jy6_22522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy6_22522/02_2024/7jy6_22522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy6_22522/02_2024/7jy6_22522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy6_22522/02_2024/7jy6_22522_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy6_22522/02_2024/7jy6_22522_trim_updated.pdb" } resolution = 2.5 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= 0.009 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 47849 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 99 5.49 5 Mg 9 5.21 5 S 116 5.16 5 C 14831 2.51 5 N 4057 2.21 5 O 4938 1.98 5 H 23799 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A GLU 18": "OE1" <-> "OE2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 94": "OD1" <-> "OD2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A ASP 110": "OD1" <-> "OD2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C ASP 110": "OD1" <-> "OD2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ASP 161": "OD1" <-> "OD2" 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 TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C ASP 276": "OD1" <-> "OD2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C GLU 325": "OE1" <-> "OE2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ASP 110": "OD1" <-> "OD2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ASP 130": "OD1" <-> "OD2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 68": "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 PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 233": "OE1" <-> "OE2" Residue "E GLU 241": "OE1" <-> "OE2" Residue "E GLU 266": "OE1" <-> "OE2" Residue "E ASP 311": "OD1" <-> "OD2" Residue "E GLU 314": "OE1" <-> "OE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 68": "OE1" <-> "OE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 100": "OD1" <-> "OD2" Residue "F ASP 110": "OD1" <-> "OD2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 235": "OE1" <-> "OE2" Residue "F ASP 276": "OD1" <-> "OD2" Residue "F ASP 311": "OD1" <-> "OD2" Residue "G GLU 18": "OE1" <-> "OE2" Residue "G GLU 31": "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 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 266": "OE1" <-> "OE2" Residue "G ASP 276": "OD1" <-> "OD2" Residue "G ASP 311": "OD1" <-> "OD2" Residue "G GLU 318": "OE1" <-> "OE2" Residue "G GLU 325": "OE1" <-> "OE2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 48": "OD1" <-> "OD2" Residue "H PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 100": "OD1" <-> "OD2" Residue "H ASP 112": "OD1" <-> "OD2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H GLU 154": "OE1" <-> "OE2" Residue "H GLU 156": "OE1" <-> "OE2" 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 233": "OE1" <-> "OE2" Residue "H GLU 241": "OE1" <-> "OE2" Residue "H ASP 276": "OD1" <-> "OD2" Residue "H GLU 285": "OE1" <-> "OE2" Residue "H TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 311": "OD1" <-> "OD2" Residue "H GLU 318": "OE1" <-> "OE2" Residue "H GLU 320": "OE1" <-> "OE2" Residue "I TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 96": "OE1" <-> "OE2" Residue "I ASP 100": "OD1" <-> "OD2" Residue "I ASP 110": "OD1" <-> "OD2" Residue "I ASP 112": "OD1" <-> "OD2" Residue "I ASP 120": "OD1" <-> "OD2" Residue "I GLU 123": "OE1" <-> "OE2" Residue "I GLU 127": "OE1" <-> "OE2" Residue "I ASP 139": "OD1" <-> "OD2" Residue "I GLU 154": "OE1" <-> "OE2" Residue "I GLU 156": "OE1" <-> "OE2" Residue "I PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 207": "OE1" <-> "OE2" 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 259": "OE1" <-> "OE2" Residue "I PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 281": "OE1" <-> "OE2" Residue "I GLU 285": "OE1" <-> "OE2" Residue "I TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 47849 Number of models: 1 Model: "" Number of chains: 20 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: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 865 Classifications: {'DNA': 27} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 26} Chain: "U" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 1441 Classifications: {'DNA': 45} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 44} 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: 15.72, per 1000 atoms: 0.33 Number of scatterers: 47849 At special positions: 0 Unit cell: (133.672, 122.892, 199.43, 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 99 15.00 Mg 9 11.99 O 4938 8.00 N 4057 7.00 C 14831 6.00 H 23799 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: 30.52 Conformation dependent library (CDL) restraints added in 3.6 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: 109 helices and 36 sheets defined 38.9% alpha, 18.7% beta 0 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 19.39 Creating SS restraints... Processing helix chain 'A' and resid 2 through 20 removed outlier: 3.781A pdb=" N LYS A 6 " --> pdb=" O ILE A 2 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 7 " --> pdb=" O ASP A 3 " (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 45 through 51 Processing helix chain 'A' and resid 72 through 86 removed outlier: 3.636A 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 167 through 185 removed outlier: 4.781A pdb=" N GLY A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 270 through 280 removed outlier: 3.589A pdb=" N ASP A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 280 " --> pdb=" O ASP A 276 " (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 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 184 removed outlier: 4.878A pdb=" N GLY B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 4.188A 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 removed outlier: 3.588A pdb=" N ASP B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 Processing helix chain 'B' and resid 313 through 327 Processing helix chain 'C' and resid 2 through 21 Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 45 through 51 Processing helix chain 'C' and resid 72 through 84 Processing helix chain 'C' and resid 101 through 107 Processing helix chain 'C' and resid 122 through 135 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 166 through 185 removed outlier: 3.574A pdb=" N ARG C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY C 180 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 4.166A 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: 3.571A 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 2 through 21 removed outlier: 3.532A pdb=" N LYS D 6 " --> pdb=" O ILE D 2 " (cutoff:3.500A) 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 122 through 135 Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 152 through 156 Processing helix chain 'D' and resid 166 through 185 removed outlier: 3.542A pdb=" N ARG D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 4.259A 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: 3.550A pdb=" N LYS E 6 " --> pdb=" O ILE E 2 " (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 86 removed outlier: 3.771A pdb=" N GLU E 86 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 107 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: 4.805A pdb=" N GLY E 180 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 4.495A 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: 3.526A pdb=" N ASP E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 310 Processing helix chain 'E' and resid 313 through 327 Processing helix chain 'F' and resid 2 through 20 removed outlier: 4.024A pdb=" N LYS F 6 " --> pdb=" O ILE F 2 " (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 45 through 51 Processing helix chain 'F' and resid 72 through 86 removed outlier: 3.523A pdb=" N GLU F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 122 through 134 Processing helix chain 'F' and resid 152 through 156 Processing helix chain 'F' and resid 166 through 185 removed outlier: 3.500A pdb=" N ARG F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS F 177 " --> pdb=" O GLN F 173 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLY F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN F 181 " --> pdb=" O LYS F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 218 Processing helix chain 'F' and resid 270 through 280 removed outlier: 3.632A pdb=" N ASP F 276 " --> pdb=" O GLY F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 311 removed outlier: 3.673A 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: 3.870A pdb=" N LYS G 6 " --> pdb=" O ILE G 2 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN G 7 " --> pdb=" O ASP G 3 " (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 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 156 Processing helix chain 'G' and resid 166 through 185 removed outlier: 3.682A pdb=" N ARG G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLY G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 4.182A 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 280 removed outlier: 3.531A 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 Processing helix chain 'H' and resid 3 through 20 removed outlier: 3.792A pdb=" N GLN H 7 " --> pdb=" O ASP H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 51 Processing helix chain 'H' and resid 72 through 85 Processing helix chain 'H' and resid 101 through 107 Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 152 through 156 Processing helix chain 'H' and resid 166 through 185 removed outlier: 3.665A pdb=" N ARG H 176 " --> pdb=" O SER H 172 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS H 177 " --> pdb=" O GLN H 173 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY H 180 " --> pdb=" O ARG H 176 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN H 181 " --> pdb=" O LYS H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 218 Processing helix chain 'H' and resid 270 through 280 Processing helix chain 'H' and resid 302 through 310 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 84 Processing helix chain 'I' and resid 101 through 107 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: 4.782A pdb=" N GLY I 180 " --> pdb=" O ARG I 176 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS I 183 " --> pdb=" O ALA I 179 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN I 184 " --> pdb=" O GLY I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 218 Processing helix chain 'I' and resid 270 through 280 removed outlier: 3.627A 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: 6.415A pdb=" N ARG A 222 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 221 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 189 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE A 64 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE A 191 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N GLY A 66 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN A 193 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A 115 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASP A 94 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 6.545A 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: 6.591A pdb=" N TYR A 293 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 5.297A 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 232 removed outlier: 3.566A pdb=" N GLY A 229 " --> pdb=" O GLU A 241 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 257 through 263 removed outlier: 6.313A pdb=" N ARG B 222 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL B 221 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 189 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE B 64 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE B 191 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N GLY B 66 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASN B 193 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.733A 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 229 through 233 removed outlier: 6.696A pdb=" N GLU B 233 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 290 through 293 removed outlier: 3.542A pdb=" N GLY B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LYS B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 257 through 263 removed outlier: 6.208A pdb=" N ARG C 222 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL C 221 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU C 189 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE C 64 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE C 191 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N GLY C 66 " --> pdb=" O PHE C 191 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASN C 193 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU C 115 " --> pdb=" O PHE C 92 " (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 removed outlier: 3.531A pdb=" N GLY C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LYS C 297 " --> pdb=" O TYR C 293 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 229 through 233 removed outlier: 3.539A pdb=" N GLY C 229 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU C 233 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.084A 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: 6.286A pdb=" N ARG D 222 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D 221 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU D 189 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE D 64 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE D 191 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N GLY D 66 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN D 193 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU D 115 " --> pdb=" O PHE D 92 " (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 229 through 233 removed outlier: 6.510A pdb=" N GLU D 233 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 290 through 293 removed outlier: 3.524A pdb=" N GLY D 299 " --> pdb=" O TYR D 291 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR D 293 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LYS D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 257 through 263 removed outlier: 6.187A pdb=" N ARG E 222 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL E 221 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU E 189 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE E 64 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE E 191 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N GLY E 66 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN E 193 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU E 115 " --> pdb=" O PHE E 92 " (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 removed outlier: 4.122A pdb=" N GLY E 299 " --> pdb=" O TYR E 291 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 229 through 233 removed outlier: 3.549A pdb=" N GLY E 229 " --> pdb=" O GLU E 241 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU E 233 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 5.727A 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: 6.235A pdb=" N ARG F 222 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL F 221 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU F 189 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE F 64 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE F 191 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLY F 66 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN F 193 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU F 115 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ASP F 94 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 6.884A 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 229 through 233 removed outlier: 6.431A pdb=" N GLU F 233 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL F 237 " --> pdb=" O GLU F 233 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 290 through 293 removed outlier: 3.746A pdb=" N GLY F 299 " --> pdb=" O TYR F 291 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TYR F 293 " --> pdb=" O LYS F 297 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LYS F 297 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 257 through 263 removed outlier: 6.267A pdb=" N ARG G 222 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL G 221 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU G 189 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE G 64 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE G 191 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N GLY G 66 " --> pdb=" O PHE G 191 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN G 193 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU G 115 " --> pdb=" O PHE G 92 " (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: 3.632A pdb=" N GLY G 299 " --> pdb=" O TYR G 291 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 229 through 233 removed outlier: 6.317A pdb=" N GLU G 233 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 6.254A 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: 6.390A pdb=" N ARG H 222 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL H 221 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU H 189 " --> pdb=" O VAL H 62 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE H 64 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE H 191 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N GLY H 66 " --> pdb=" O PHE H 191 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASN H 193 " --> pdb=" O GLY H 66 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU H 115 " --> pdb=" O PHE H 92 " (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 229 through 233 removed outlier: 6.557A pdb=" N GLU H 233 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL H 237 " --> pdb=" O GLU H 233 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 290 through 293 removed outlier: 6.434A pdb=" N TYR H 293 " --> pdb=" O LYS H 297 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS H 297 " --> pdb=" O TYR H 293 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 257 through 263 removed outlier: 6.672A pdb=" N ARG I 222 " --> pdb=" O VAL I 247 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL I 221 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU I 189 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE I 64 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHE I 191 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLY I 66 " --> pdb=" O PHE I 191 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN I 193 " --> pdb=" O GLY I 66 " (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 Processing sheet with id= AJ, first strand: chain 'I' and resid 229 through 232 968 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 16.26 Time building geometry restraints manager: 32.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.09: 23273 1.09 - 1.34: 6629 1.34 - 1.58: 17993 1.58 - 1.83: 352 1.83 - 2.07: 13 Bond restraints: 48260 Sorted by residual: bond pdb=" C4 AGS C 402 " pdb=" C5 AGS C 402 " ideal model delta sigma weight residual 1.386 1.482 -0.096 1.00e-02 1.00e+04 9.26e+01 bond pdb=" C4 AGS I 402 " pdb=" C5 AGS I 402 " ideal model delta sigma weight residual 1.386 1.476 -0.090 1.00e-02 1.00e+04 8.16e+01 bond pdb=" N3 DT U 10 " pdb=" H3 DT U 10 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.16e+01 bond pdb=" N3 DT U 38 " pdb=" H3 DT U 38 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.15e+01 bond pdb=" N3 DT S 7 " pdb=" H3 DT S 7 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.15e+01 ... (remaining 48255 not shown) Histogram of bond angle deviations from ideal: 94.25 - 102.96: 317 102.96 - 111.67: 54683 111.67 - 120.38: 23795 120.38 - 129.09: 8855 129.09 - 137.80: 92 Bond angle restraints: 87742 Sorted by residual: angle pdb=" C5 AGS I 402 " pdb=" C4 AGS I 402 " pdb=" N3 AGS I 402 " ideal model delta sigma weight residual 126.80 118.31 8.49 7.41e-01 1.82e+00 1.31e+02 angle pdb=" C5 AGS G 402 " pdb=" C4 AGS G 402 " pdb=" N3 AGS G 402 " ideal model delta sigma weight residual 126.80 118.49 8.31 7.41e-01 1.82e+00 1.26e+02 angle pdb=" C5 AGS D 402 " pdb=" N7 AGS D 402 " pdb=" C8 AGS D 402 " ideal model delta sigma weight residual 103.67 108.26 -4.59 4.26e-01 5.51e+00 1.16e+02 angle pdb=" C5 AGS A 402 " pdb=" C4 AGS A 402 " pdb=" N3 AGS A 402 " ideal model delta sigma weight residual 126.80 118.83 7.97 7.41e-01 1.82e+00 1.16e+02 angle pdb=" C5 AGS H 402 " pdb=" C4 AGS H 402 " pdb=" N3 AGS H 402 " ideal model delta sigma weight residual 126.80 118.86 7.94 7.41e-01 1.82e+00 1.15e+02 ... (remaining 87737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 20625 34.38 - 68.75: 1301 68.75 - 103.13: 39 103.13 - 137.50: 4 137.50 - 171.88: 9 Dihedral angle restraints: 21978 sinusoidal: 12849 harmonic: 9129 Sorted by residual: dihedral pdb=" CA ASP D 144 " pdb=" C ASP D 144 " pdb=" N SER D 145 " pdb=" CA SER D 145 " ideal model delta harmonic sigma weight residual 180.00 108.96 71.04 0 5.00e+00 4.00e-02 2.02e+02 dihedral pdb=" CA ASP E 144 " pdb=" C ASP E 144 " pdb=" N SER E 145 " pdb=" CA SER E 145 " ideal model delta harmonic sigma weight residual 180.00 147.47 32.53 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA SER B 145 " pdb=" C SER B 145 " pdb=" N VAL B 146 " pdb=" CA VAL B 146 " ideal model delta harmonic sigma weight residual 180.00 149.47 30.53 0 5.00e+00 4.00e-02 3.73e+01 ... (remaining 21975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2400 0.088 - 0.176: 1246 0.176 - 0.264: 162 0.264 - 0.352: 19 0.352 - 0.440: 8 Chirality restraints: 3835 Sorted by residual: 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 2.07 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA SER E 145 " pdb=" N SER E 145 " pdb=" C SER E 145 " pdb=" CB SER E 145 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CB VAL C 79 " pdb=" CA VAL C 79 " pdb=" CG1 VAL C 79 " pdb=" CG2 VAL C 79 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 3832 not shown) Planarity restraints: 6906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 144 " 0.026 2.00e-02 2.50e+03 5.68e-02 3.22e+01 pdb=" C ASP D 144 " -0.098 2.00e-02 2.50e+03 pdb=" O ASP D 144 " 0.038 2.00e-02 2.50e+03 pdb=" N SER D 145 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 144 " -0.022 2.00e-02 2.50e+03 4.85e-02 2.35e+01 pdb=" C ASP G 144 " 0.084 2.00e-02 2.50e+03 pdb=" O ASP G 144 " -0.034 2.00e-02 2.50e+03 pdb=" N SER G 145 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 144 " -0.019 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C ASP F 144 " 0.072 2.00e-02 2.50e+03 pdb=" O ASP F 144 " -0.029 2.00e-02 2.50e+03 pdb=" N SER F 145 " -0.024 2.00e-02 2.50e+03 ... (remaining 6903 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.94: 293 1.94 - 2.60: 47696 2.60 - 3.27: 140962 3.27 - 3.93: 181118 3.93 - 4.60: 280422 Nonbonded interactions: 650491 Sorted by model distance: nonbonded pdb="HH11 ARG G 60 " pdb=" HG SER G 220 " model vdw 1.273 2.100 nonbonded pdb="HH11 ARG C 60 " pdb=" HG SER C 220 " model vdw 1.376 2.100 nonbonded pdb="HH11 ARG B 60 " pdb=" HG SER B 220 " model vdw 1.388 2.100 nonbonded pdb=" OE1 GLU G 63 " pdb="HH11 ARG G 222 " model vdw 1.464 1.850 nonbonded pdb=" O ALA E 133 " pdb=" HG SER E 185 " model vdw 1.510 1.850 ... (remaining 650486 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.450 Construct map_model_manager: 0.530 Extract box with map and model: 5.530 Check model and map are aligned: 0.530 Set scattering table: 0.330 Process input model: 132.450 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.120 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:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 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 0.163 24461 Z= 0.924 Angle : 1.923 16.256 33293 Z= 1.400 Chirality : 0.095 0.440 3835 Planarity : 0.005 0.057 4032 Dihedral : 19.774 171.879 9442 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.70 % Favored : 95.96 % Rotamer: Outliers : 5.06 % Allowed : 9.17 % Favored : 85.78 % Cbeta Deviations : 0.30 % 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: -2.63 (0.13), residues: 2946 helix: -1.99 (0.11), residues: 1289 sheet: 0.47 (0.22), residues: 479 loop : -2.30 (0.14), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 290 HIS 0.008 0.003 HIS C 97 PHE 0.026 0.004 PHE I 270 TYR 0.036 0.004 TYR B 218 ARG 0.022 0.002 ARG E 176 *********************** 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 495 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 377 time to evaluate : 2.780 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: A 78 GLN cc_start: 0.6641 (mm-40) cc_final: 0.6335 (mm-40) REVERT: A 124 GLN cc_start: 0.4609 (tt0) cc_final: 0.4318 (mm-40) REVERT: B 23 LYS cc_start: 0.6838 (tmmm) cc_final: 0.6248 (tmmt) REVERT: B 118 GLN cc_start: 0.7544 (mt0) cc_final: 0.7336 (mt0) REVERT: B 164 MET cc_start: 0.5874 (mtm) cc_final: 0.5634 (mmp) REVERT: B 171 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7766 (mmm) REVERT: C 8 LYS cc_start: 0.7855 (mtmt) cc_final: 0.7605 (tmtt) REVERT: C 68 GLU cc_start: 0.8315 (pm20) cc_final: 0.8113 (pm20) REVERT: C 161 ASP cc_start: 0.7512 (m-30) cc_final: 0.7135 (m-30) REVERT: D 96 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7911 (mt-10) REVERT: D 245 LYS cc_start: 0.8279 (mttp) cc_final: 0.7927 (mtpp) REVERT: E 20 GLN cc_start: 0.7824 (tt0) cc_final: 0.7508 (tt0) REVERT: E 68 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7115 (pp20) REVERT: E 189 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9019 (tt) REVERT: E 250 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8884 (mttt) REVERT: F 149 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8720 (mt) REVERT: F 152 LYS cc_start: 0.8347 (tttm) cc_final: 0.8054 (ttpp) REVERT: F 189 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8746 (tt) REVERT: F 250 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8394 (mttt) REVERT: F 291 TYR cc_start: 0.6616 (m-80) cc_final: 0.6301 (m-10) REVERT: G 27 MET cc_start: 0.6678 (ptp) cc_final: 0.6454 (ptp) REVERT: I 202 MET cc_start: 0.0837 (mpp) cc_final: -0.0077 (ptm) outliers start: 118 outliers final: 35 residues processed: 477 average time/residue: 2.3471 time to fit residues: 1291.3991 Evaluate side-chains 286 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 244 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain I residue 273 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 235 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 272 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 113 ASN B 7 GLN B 124 GLN B 236 ASN D 20 GLN D 332 ASN E 16 GLN E 20 GLN E 184 GLN E 257 GLN H 124 GLN H 304 ASN I 194 GLN I 312 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24461 Z= 0.190 Angle : 0.621 6.085 33293 Z= 0.347 Chirality : 0.041 0.148 3835 Planarity : 0.004 0.058 4032 Dihedral : 19.224 178.079 4109 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.70 % Favored : 98.07 % Rotamer: Outliers : 2.91 % Allowed : 15.60 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 2946 helix: 0.42 (0.14), residues: 1293 sheet: 0.71 (0.22), residues: 512 loop : -1.99 (0.15), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 290 HIS 0.005 0.001 HIS A 97 PHE 0.013 0.001 PHE I 270 TYR 0.010 0.001 TYR F 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 334 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 266 time to evaluate : 2.739 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: A 33 ARG cc_start: 0.5954 (mmp80) cc_final: 0.5672 (mmp-170) REVERT: A 48 ASP cc_start: 0.5650 (m-30) cc_final: 0.5345 (m-30) REVERT: A 68 GLU cc_start: 0.4279 (OUTLIER) cc_final: 0.3695 (mm-30) REVERT: A 124 GLN cc_start: 0.4594 (tt0) cc_final: 0.4355 (mm-40) REVERT: A 292 SER cc_start: 0.3269 (m) cc_final: 0.2543 (t) REVERT: B 118 GLN cc_start: 0.7559 (mt0) cc_final: 0.7267 (mt0) REVERT: B 164 MET cc_start: 0.5792 (mtm) cc_final: 0.5496 (mmp) REVERT: B 171 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7564 (mmm) REVERT: C 8 LYS cc_start: 0.7741 (mtmt) cc_final: 0.7454 (tmtt) REVERT: C 23 LYS cc_start: 0.7664 (tttm) cc_final: 0.7423 (ttpp) REVERT: C 161 ASP cc_start: 0.7832 (m-30) cc_final: 0.7420 (m-30) REVERT: D 6 LYS cc_start: 0.7543 (mtpt) cc_final: 0.7324 (mttp) REVERT: D 96 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7788 (mt-10) REVERT: D 184 GLN cc_start: 0.7920 (tp40) cc_final: 0.7700 (mm-40) REVERT: D 209 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8009 (p) REVERT: D 290 TRP cc_start: 0.5963 (m100) cc_final: 0.5507 (m100) REVERT: D 315 THR cc_start: 0.7498 (OUTLIER) cc_final: 0.7289 (m) REVERT: E 18 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7306 (mm-30) REVERT: E 19 LYS cc_start: 0.8234 (mmmt) cc_final: 0.7841 (tmmt) REVERT: E 35 MET cc_start: 0.8869 (mmm) cc_final: 0.8555 (mmm) REVERT: E 68 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7312 (pp20) REVERT: E 209 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7890 (p) REVERT: F 19 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8101 (ttmm) REVERT: F 149 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8722 (mt) REVERT: F 152 LYS cc_start: 0.8418 (tttm) cc_final: 0.7953 (ttpp) REVERT: G 27 MET cc_start: 0.6716 (ptp) cc_final: 0.6456 (ptp) REVERT: H 282 LYS cc_start: 0.5010 (mmtt) cc_final: 0.4499 (mtpm) REVERT: I 202 MET cc_start: 0.0926 (mpp) cc_final: 0.0002 (ptm) outliers start: 68 outliers final: 32 residues processed: 321 average time/residue: 2.3892 time to fit residues: 884.8952 Evaluate side-chains 273 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 233 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 202 MET Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 268 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 272 optimal weight: 30.0000 chunk 294 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 270 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 218 optimal weight: 0.0040 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 ASN H 7 GLN I 113 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 24461 Z= 0.278 Angle : 0.640 7.072 33293 Z= 0.347 Chirality : 0.046 0.224 3835 Planarity : 0.004 0.048 4032 Dihedral : 18.817 177.073 4083 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.00 % Favored : 97.83 % Rotamer: Outliers : 3.00 % Allowed : 16.58 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.19 (0.14), residues: 2946 helix: 0.96 (0.14), residues: 1291 sheet: 0.86 (0.22), residues: 512 loop : -1.92 (0.15), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 290 HIS 0.005 0.001 HIS H 97 PHE 0.014 0.002 PHE E 191 TYR 0.019 0.002 TYR E 218 ARG 0.005 0.001 ARG E 196 *********************** 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 316 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 246 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6054 (mmp80) cc_final: 0.5769 (mmp-170) REVERT: A 68 GLU cc_start: 0.4481 (OUTLIER) cc_final: 0.3752 (mm-30) REVERT: A 124 GLN cc_start: 0.5018 (tt0) cc_final: 0.4384 (mm-40) REVERT: B 118 GLN cc_start: 0.7627 (mt0) cc_final: 0.7280 (mt0) REVERT: B 171 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7701 (mmm) REVERT: C 8 LYS cc_start: 0.7791 (mtmt) cc_final: 0.7461 (tmtt) REVERT: C 20 GLN cc_start: 0.8107 (tt0) cc_final: 0.7869 (tt0) REVERT: C 161 ASP cc_start: 0.7683 (m-30) cc_final: 0.7360 (m-30) REVERT: D 6 LYS cc_start: 0.7523 (mtpt) cc_final: 0.7311 (mttp) REVERT: D 58 MET cc_start: 0.8330 (mmm) cc_final: 0.7960 (mmm) REVERT: D 96 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7747 (mt-10) REVERT: D 164 MET cc_start: 0.7570 (mmt) cc_final: 0.7151 (mmt) REVERT: D 184 GLN cc_start: 0.7875 (tp40) cc_final: 0.7625 (mm110) REVERT: D 226 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8258 (mtt-85) REVERT: D 290 TRP cc_start: 0.6116 (m100) cc_final: 0.5666 (m100) REVERT: D 315 THR cc_start: 0.7572 (OUTLIER) cc_final: 0.7339 (m) REVERT: E 18 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7418 (mm-30) REVERT: E 19 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7896 (ttpp) REVERT: E 23 LYS cc_start: 0.6280 (OUTLIER) cc_final: 0.5747 (tmtt) REVERT: E 35 MET cc_start: 0.8910 (mmm) cc_final: 0.8623 (mmm) REVERT: E 68 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7218 (pp20) REVERT: F 19 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8089 (ttmm) REVERT: F 152 LYS cc_start: 0.8458 (tttm) cc_final: 0.7973 (ttpp) REVERT: G 27 MET cc_start: 0.6764 (ptp) cc_final: 0.6490 (ptp) REVERT: G 271 TYR cc_start: 0.6285 (m-10) cc_final: 0.5927 (m-10) REVERT: H 282 LYS cc_start: 0.5075 (mmtt) cc_final: 0.4681 (mtpm) outliers start: 70 outliers final: 48 residues processed: 299 average time/residue: 2.3087 time to fit residues: 800.8918 Evaluate side-chains 291 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 236 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 5 ASN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 226 ARG Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 202 MET Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 268 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 20.0000 chunk 205 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 130 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 273 optimal weight: 10.0000 chunk 289 optimal weight: 20.0000 chunk 143 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN E 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24461 Z= 0.213 Angle : 0.583 6.651 33293 Z= 0.320 Chirality : 0.043 0.164 3835 Planarity : 0.004 0.072 4032 Dihedral : 18.754 177.920 4080 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.53 % Favored : 98.37 % Rotamer: Outliers : 2.91 % Allowed : 16.92 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.08 (0.14), residues: 2946 helix: 1.35 (0.14), residues: 1275 sheet: 0.88 (0.22), residues: 514 loop : -1.88 (0.14), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 290 HIS 0.004 0.001 HIS I 97 PHE 0.013 0.001 PHE E 191 TYR 0.010 0.001 TYR E 218 ARG 0.005 0.000 ARG H 134 *********************** 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 312 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 244 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6080 (mmp80) cc_final: 0.5794 (mmp-170) REVERT: A 124 GLN cc_start: 0.5003 (tt0) cc_final: 0.4304 (mm-40) REVERT: B 118 GLN cc_start: 0.7636 (mt0) cc_final: 0.7319 (mt0) REVERT: B 171 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7827 (mmm) REVERT: B 175 MET cc_start: 0.8519 (mmp) cc_final: 0.8137 (mmp) REVERT: C 8 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7417 (tmtt) REVERT: C 19 LYS cc_start: 0.7698 (ttmp) cc_final: 0.7372 (mtmt) REVERT: C 20 GLN cc_start: 0.8225 (tt0) cc_final: 0.7992 (tt0) REVERT: C 161 ASP cc_start: 0.7726 (m-30) cc_final: 0.7450 (m-30) REVERT: D 6 LYS cc_start: 0.7485 (mtpt) cc_final: 0.7260 (mttp) REVERT: D 8 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7385 (tttp) REVERT: D 58 MET cc_start: 0.8357 (mmm) cc_final: 0.7921 (mmm) REVERT: D 96 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7690 (mt-10) REVERT: D 164 MET cc_start: 0.7528 (mmt) cc_final: 0.7161 (mmt) REVERT: D 226 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8318 (mtt-85) REVERT: D 290 TRP cc_start: 0.6084 (m100) cc_final: 0.5611 (m100) REVERT: D 315 THR cc_start: 0.7643 (OUTLIER) cc_final: 0.7406 (m) REVERT: E 8 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7753 (mtpt) REVERT: E 19 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7967 (ttpp) REVERT: E 68 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7588 (pp20) REVERT: E 145 SER cc_start: 0.8042 (OUTLIER) cc_final: 0.7481 (t) REVERT: E 247 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8595 (t) REVERT: F 19 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8091 (ttmm) REVERT: G 27 MET cc_start: 0.6893 (ptp) cc_final: 0.6627 (ptp) REVERT: G 271 TYR cc_start: 0.6326 (m-10) cc_final: 0.5908 (m-10) REVERT: H 282 LYS cc_start: 0.5112 (mmtt) cc_final: 0.4734 (mtpm) outliers start: 68 outliers final: 41 residues processed: 292 average time/residue: 2.3857 time to fit residues: 810.9752 Evaluate side-chains 282 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 232 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 226 ARG Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 268 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 148 optimal weight: 2.9990 chunk 260 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 24461 Z= 0.320 Angle : 0.664 9.778 33293 Z= 0.356 Chirality : 0.047 0.228 3835 Planarity : 0.004 0.060 4032 Dihedral : 18.693 173.601 4079 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.65 % Favored : 97.22 % Rotamer: Outliers : 3.81 % Allowed : 16.28 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.08 (0.14), residues: 2946 helix: 1.15 (0.14), residues: 1275 sheet: 0.82 (0.22), residues: 514 loop : -1.90 (0.14), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 290 HIS 0.005 0.001 HIS I 97 PHE 0.017 0.002 PHE E 191 TYR 0.020 0.002 TYR E 218 ARG 0.005 0.001 ARG E 196 *********************** 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 324 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 235 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6186 (mmp80) cc_final: 0.5778 (mmp-170) REVERT: A 68 GLU cc_start: 0.5319 (OUTLIER) cc_final: 0.4530 (mt-10) REVERT: A 124 GLN cc_start: 0.5136 (tt0) cc_final: 0.4399 (mm-40) REVERT: B 118 GLN cc_start: 0.7635 (mt0) cc_final: 0.7315 (mt0) REVERT: B 171 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7860 (mmm) REVERT: C 8 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7625 (tmtt) REVERT: D 8 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7444 (tppt) REVERT: D 96 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7720 (mt-10) REVERT: D 164 MET cc_start: 0.7529 (mmt) cc_final: 0.7246 (mmt) REVERT: D 226 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8232 (mtt-85) REVERT: D 290 TRP cc_start: 0.6030 (m100) cc_final: 0.5554 (m100) REVERT: D 315 THR cc_start: 0.7602 (OUTLIER) cc_final: 0.7373 (m) REVERT: E 19 LYS cc_start: 0.8223 (mmmt) cc_final: 0.7975 (ttpp) REVERT: E 68 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7307 (pp20) REVERT: E 145 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.7857 (t) REVERT: E 247 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8611 (t) REVERT: F 19 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8142 (ttmm) REVERT: F 317 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.6260 (mtpt) REVERT: G 27 MET cc_start: 0.6993 (ptp) cc_final: 0.6783 (ptp) REVERT: G 271 TYR cc_start: 0.6460 (m-10) cc_final: 0.5982 (m-10) REVERT: H 259 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: H 282 LYS cc_start: 0.5293 (mmtt) cc_final: 0.4887 (mtpm) REVERT: I 171 MET cc_start: 0.3231 (tpt) cc_final: 0.2467 (mmm) REVERT: I 202 MET cc_start: 0.0751 (mpt) cc_final: -0.0020 (tmm) outliers start: 89 outliers final: 54 residues processed: 307 average time/residue: 2.3310 time to fit residues: 841.2136 Evaluate side-chains 291 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 226 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 5 ASN Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 226 ARG Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain H residue 259 GLU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 268 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 290 optimal weight: 9.9990 chunk 240 optimal weight: 9.9990 chunk 134 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN F 20 GLN H 213 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24461 Z= 0.229 Angle : 0.583 7.617 33293 Z= 0.319 Chirality : 0.044 0.165 3835 Planarity : 0.004 0.085 4032 Dihedral : 18.680 170.490 4079 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.80 % Favored : 98.13 % Rotamer: Outliers : 2.96 % Allowed : 17.74 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.09 (0.15), residues: 2946 helix: 1.35 (0.14), residues: 1275 sheet: 0.84 (0.22), residues: 508 loop : -1.84 (0.15), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 290 HIS 0.004 0.001 HIS I 97 PHE 0.013 0.001 PHE E 191 TYR 0.013 0.001 TYR E 218 ARG 0.009 0.000 ARG H 134 *********************** 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 300 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 231 time to evaluate : 2.780 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: A 78 GLN cc_start: 0.6920 (mm-40) cc_final: 0.5306 (tp-100) REVERT: A 124 GLN cc_start: 0.5214 (tt0) cc_final: 0.4407 (mm-40) REVERT: B 118 GLN cc_start: 0.7608 (mt0) cc_final: 0.7271 (mt0) REVERT: C 8 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7629 (tmtt) REVERT: C 19 LYS cc_start: 0.7783 (ttmp) cc_final: 0.7423 (mtmt) REVERT: C 105 ARG cc_start: 0.8318 (ttm170) cc_final: 0.8116 (ttm170) REVERT: D 7 GLN cc_start: 0.7987 (mt0) cc_final: 0.7774 (mt0) REVERT: D 8 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7348 (tttp) REVERT: D 96 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7690 (mt-10) REVERT: D 164 MET cc_start: 0.7527 (mmt) cc_final: 0.7285 (mmt) REVERT: D 226 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8109 (mtt-85) REVERT: D 290 TRP cc_start: 0.6015 (m100) cc_final: 0.5548 (m100) REVERT: D 315 THR cc_start: 0.7676 (OUTLIER) cc_final: 0.7426 (m) REVERT: E 8 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7741 (mtpt) REVERT: E 19 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7915 (ttpp) REVERT: E 68 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7593 (pp20) REVERT: E 247 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8598 (t) REVERT: F 19 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8125 (ttmm) REVERT: G 27 MET cc_start: 0.7044 (ptp) cc_final: 0.6838 (ptp) REVERT: G 271 TYR cc_start: 0.6516 (m-10) cc_final: 0.6045 (m-10) REVERT: H 79 VAL cc_start: 0.7960 (OUTLIER) cc_final: 0.7468 (m) REVERT: H 175 MET cc_start: 0.6369 (OUTLIER) cc_final: 0.5791 (tpt) REVERT: I 35 MET cc_start: 0.2302 (mpt) cc_final: 0.1589 (mtp) REVERT: I 202 MET cc_start: 0.0775 (mpt) cc_final: 0.0000 (tmm) outliers start: 69 outliers final: 47 residues processed: 286 average time/residue: 2.2640 time to fit residues: 753.7342 Evaluate side-chains 283 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 227 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 226 ARG Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain I residue 273 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 289 optimal weight: 20.0000 chunk 180 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24461 Z= 0.194 Angle : 0.556 6.151 33293 Z= 0.305 Chirality : 0.043 0.175 3835 Planarity : 0.004 0.073 4032 Dihedral : 18.579 169.043 4071 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.96 % Rotamer: Outliers : 2.91 % Allowed : 17.95 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.28 (0.15), residues: 2946 helix: 1.56 (0.14), residues: 1275 sheet: 0.88 (0.22), residues: 508 loop : -1.78 (0.15), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 290 HIS 0.003 0.001 HIS I 97 PHE 0.013 0.001 PHE E 191 TYR 0.010 0.001 TYR E 218 ARG 0.008 0.000 ARG H 134 *********************** 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 297 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 229 time to evaluate : 2.766 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: A 78 GLN cc_start: 0.6939 (mm-40) cc_final: 0.5309 (tp-100) REVERT: A 124 GLN cc_start: 0.5226 (tt0) cc_final: 0.4418 (mm-40) REVERT: C 8 LYS cc_start: 0.7913 (mtmt) cc_final: 0.7613 (tmtt) REVERT: C 19 LYS cc_start: 0.7749 (ttmp) cc_final: 0.7389 (mtmt) REVERT: D 7 GLN cc_start: 0.7986 (mt0) cc_final: 0.7777 (mt0) REVERT: D 8 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7400 (tppt) REVERT: D 19 LYS cc_start: 0.7634 (pttm) cc_final: 0.7089 (tptp) REVERT: D 96 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7681 (mt-10) REVERT: D 164 MET cc_start: 0.7542 (mmt) cc_final: 0.7192 (mmt) REVERT: D 226 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8329 (mtt-85) REVERT: D 238 VAL cc_start: 0.8340 (p) cc_final: 0.8115 (m) REVERT: D 245 LYS cc_start: 0.7975 (mttp) cc_final: 0.7728 (mtpp) REVERT: D 290 TRP cc_start: 0.5997 (m100) cc_final: 0.5521 (m100) REVERT: D 315 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7405 (m) REVERT: E 8 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7731 (mtpt) REVERT: E 19 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7929 (ttpp) REVERT: E 68 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7637 (pp20) REVERT: E 145 SER cc_start: 0.7257 (m) cc_final: 0.6860 (t) REVERT: F 19 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8118 (ttmm) REVERT: H 79 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7286 (m) REVERT: H 175 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.5783 (tpt) REVERT: I 35 MET cc_start: 0.2299 (mpt) cc_final: 0.1714 (mtt) REVERT: I 202 MET cc_start: 0.0789 (mpt) cc_final: 0.0005 (tmm) REVERT: I 209 THR cc_start: 0.5065 (OUTLIER) cc_final: 0.4818 (p) REVERT: I 216 LYS cc_start: 0.3502 (OUTLIER) cc_final: 0.3253 (pptt) outliers start: 68 outliers final: 47 residues processed: 283 average time/residue: 2.2391 time to fit residues: 739.1464 Evaluate side-chains 283 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 226 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 5 ASN Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 226 ARG Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 175 MET Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 268 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 26 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 263 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN F 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24461 Z= 0.192 Angle : 0.552 6.554 33293 Z= 0.303 Chirality : 0.042 0.153 3835 Planarity : 0.003 0.041 4032 Dihedral : 18.544 167.856 4070 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.70 % Allowed : 18.08 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 2946 helix: 1.62 (0.14), residues: 1275 sheet: 0.92 (0.22), residues: 508 loop : -1.75 (0.15), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 290 HIS 0.003 0.001 HIS I 97 PHE 0.014 0.001 PHE E 191 TYR 0.011 0.001 TYR E 218 ARG 0.003 0.000 ARG E 196 *********************** 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 294 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 231 time to evaluate : 2.817 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 78 GLN cc_start: 0.6944 (mm-40) cc_final: 0.5307 (tp-100) REVERT: A 124 GLN cc_start: 0.5276 (tt0) cc_final: 0.4451 (mm-40) REVERT: C 8 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7609 (tmtt) REVERT: C 19 LYS cc_start: 0.7749 (ttmp) cc_final: 0.7394 (mtmt) REVERT: D 7 GLN cc_start: 0.7990 (mt0) cc_final: 0.7779 (mt0) REVERT: D 8 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7403 (tppt) REVERT: D 19 LYS cc_start: 0.7633 (pttm) cc_final: 0.7094 (tptp) REVERT: D 96 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7692 (mt-10) REVERT: D 164 MET cc_start: 0.7542 (mmt) cc_final: 0.7222 (mmt) REVERT: D 226 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8329 (mtt-85) REVERT: D 245 LYS cc_start: 0.7973 (mttp) cc_final: 0.7732 (mtpp) REVERT: D 290 TRP cc_start: 0.5947 (m100) cc_final: 0.5509 (m100) REVERT: D 315 THR cc_start: 0.7668 (OUTLIER) cc_final: 0.7407 (m) REVERT: E 19 LYS cc_start: 0.8145 (mmmt) cc_final: 0.7925 (ttpp) REVERT: E 68 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7639 (pp20) REVERT: E 145 SER cc_start: 0.7396 (m) cc_final: 0.7019 (t) REVERT: F 19 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8149 (ttmm) REVERT: H 79 VAL cc_start: 0.7739 (OUTLIER) cc_final: 0.7277 (m) REVERT: H 175 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.5797 (tpt) REVERT: I 35 MET cc_start: 0.2281 (mpt) cc_final: 0.1648 (mtt) REVERT: I 202 MET cc_start: 0.0802 (mpt) cc_final: 0.0023 (tmm) REVERT: I 209 THR cc_start: 0.5098 (OUTLIER) cc_final: 0.4852 (p) REVERT: I 216 LYS cc_start: 0.3492 (OUTLIER) cc_final: 0.3247 (pptt) outliers start: 63 outliers final: 47 residues processed: 282 average time/residue: 2.2691 time to fit residues: 747.0391 Evaluate side-chains 285 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 229 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 226 ARG Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 175 MET Chi-restraints excluded: chain I residue 197 MET Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain I residue 273 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 30.0000 chunk 252 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 chunk 276 optimal weight: 0.0470 chunk 162 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 243 optimal weight: 9.9990 chunk 254 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN F 300 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24461 Z= 0.274 Angle : 0.618 8.600 33293 Z= 0.333 Chirality : 0.045 0.215 3835 Planarity : 0.004 0.050 4032 Dihedral : 18.573 166.247 4068 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.83 % Allowed : 18.17 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.17 (0.15), residues: 2946 helix: 1.40 (0.14), residues: 1275 sheet: 0.91 (0.23), residues: 504 loop : -1.77 (0.15), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 290 HIS 0.004 0.001 HIS I 97 PHE 0.018 0.002 PHE E 191 TYR 0.016 0.002 TYR E 218 ARG 0.004 0.001 ARG C 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 302 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 236 time to evaluate : 2.823 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: A 78 GLN cc_start: 0.6965 (mm-40) cc_final: 0.5346 (tp-100) REVERT: A 124 GLN cc_start: 0.5316 (tt0) cc_final: 0.4556 (mm-40) REVERT: C 8 LYS cc_start: 0.7934 (mtmt) cc_final: 0.7666 (tmtt) REVERT: C 19 LYS cc_start: 0.7749 (ttmp) cc_final: 0.7403 (mtmt) REVERT: D 7 GLN cc_start: 0.8069 (mt0) cc_final: 0.7865 (mt0) REVERT: D 8 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7432 (tppt) REVERT: D 96 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7717 (mt-10) REVERT: D 164 MET cc_start: 0.7522 (mmt) cc_final: 0.7230 (mmt) REVERT: D 226 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8241 (mtt-85) REVERT: D 245 LYS cc_start: 0.8039 (mttp) cc_final: 0.7774 (mtpp) REVERT: D 290 TRP cc_start: 0.5938 (m100) cc_final: 0.5490 (m100) REVERT: D 315 THR cc_start: 0.7614 (OUTLIER) cc_final: 0.7363 (m) REVERT: E 8 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7767 (mtpt) REVERT: E 19 LYS cc_start: 0.8132 (mmmt) cc_final: 0.7916 (ttpp) REVERT: E 68 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7598 (pp20) REVERT: F 183 LYS cc_start: 0.8358 (tppp) cc_final: 0.7915 (tmtt) REVERT: H 63 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6639 (tt0) REVERT: H 79 VAL cc_start: 0.7806 (OUTLIER) cc_final: 0.7350 (m) REVERT: H 175 MET cc_start: 0.6373 (OUTLIER) cc_final: 0.5864 (tpt) REVERT: H 324 ARG cc_start: 0.5920 (mtp180) cc_final: 0.5577 (mtp180) REVERT: I 35 MET cc_start: 0.2417 (mpt) cc_final: 0.1197 (ptp) REVERT: I 202 MET cc_start: 0.0834 (mpt) cc_final: 0.0046 (tmm) REVERT: I 216 LYS cc_start: 0.3541 (OUTLIER) cc_final: 0.3272 (pptt) outliers start: 66 outliers final: 49 residues processed: 290 average time/residue: 2.3406 time to fit residues: 796.7941 Evaluate side-chains 286 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 228 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 226 ARG Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 175 MET Chi-restraints excluded: chain I residue 197 MET Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 273 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 275 optimal weight: 20.0000 chunk 237 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN F 20 GLN F 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24461 Z= 0.289 Angle : 0.626 8.672 33293 Z= 0.337 Chirality : 0.045 0.202 3835 Planarity : 0.005 0.133 4032 Dihedral : 18.631 167.816 4066 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.57 % Allowed : 18.59 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.09 (0.15), residues: 2946 helix: 1.30 (0.14), residues: 1275 sheet: 0.86 (0.23), residues: 504 loop : -1.77 (0.15), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 290 HIS 0.005 0.001 HIS F 97 PHE 0.016 0.002 PHE E 191 TYR 0.017 0.002 TYR E 218 ARG 0.017 0.001 ARG H 134 ********************** 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 290 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 230 time to evaluate : 2.794 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: A 78 GLN cc_start: 0.6974 (mm-40) cc_final: 0.5371 (tp-100) REVERT: A 124 GLN cc_start: 0.5333 (tt0) cc_final: 0.4529 (mm-40) REVERT: B 35 MET cc_start: 0.8339 (mmm) cc_final: 0.8117 (mmm) REVERT: C 8 LYS cc_start: 0.7940 (mtmt) cc_final: 0.7662 (tmtt) REVERT: C 19 LYS cc_start: 0.7698 (ttmp) cc_final: 0.7363 (mtmt) REVERT: D 7 GLN cc_start: 0.8082 (mt0) cc_final: 0.7865 (mt0) REVERT: D 8 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7440 (tppt) REVERT: D 96 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7703 (mt-10) REVERT: D 164 MET cc_start: 0.7544 (mmt) cc_final: 0.7245 (mmt) REVERT: D 226 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8116 (mtt-85) REVERT: D 245 LYS cc_start: 0.8044 (mttp) cc_final: 0.7775 (mtpp) REVERT: D 290 TRP cc_start: 0.5925 (m100) cc_final: 0.5486 (m100) REVERT: D 315 THR cc_start: 0.7627 (OUTLIER) cc_final: 0.7379 (m) REVERT: E 8 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7795 (mtpt) REVERT: E 68 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7600 (pp20) REVERT: F 19 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8180 (ttmm) REVERT: F 183 LYS cc_start: 0.8354 (tppp) cc_final: 0.7910 (tmtt) REVERT: H 79 VAL cc_start: 0.7774 (OUTLIER) cc_final: 0.7354 (m) REVERT: H 175 MET cc_start: 0.6296 (OUTLIER) cc_final: 0.5918 (tpt) REVERT: H 324 ARG cc_start: 0.5925 (mtp180) cc_final: 0.5576 (mtp180) REVERT: I 35 MET cc_start: 0.2562 (mpt) cc_final: 0.1301 (ptp) REVERT: I 202 MET cc_start: 0.0866 (mpt) cc_final: 0.0064 (tmm) outliers start: 60 outliers final: 50 residues processed: 277 average time/residue: 2.2951 time to fit residues: 738.6911 Evaluate side-chains 284 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 226 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 226 ARG Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain I residue 175 MET Chi-restraints excluded: chain I residue 216 LYS Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 273 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 238 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 30 optimal weight: 30.0000 chunk 43 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN H 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.233379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.194210 restraints weight = 62954.892| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 1.46 r_work: 0.3857 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24461 Z= 0.298 Angle : 0.636 9.149 33293 Z= 0.342 Chirality : 0.046 0.210 3835 Planarity : 0.004 0.048 4032 Dihedral : 18.652 166.813 4066 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 2.83 % Allowed : 18.59 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.04 (0.15), residues: 2946 helix: 1.24 (0.14), residues: 1275 sheet: 0.85 (0.23), residues: 504 loop : -1.78 (0.15), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 290 HIS 0.004 0.001 HIS D 163 PHE 0.018 0.002 PHE E 191 TYR 0.018 0.002 TYR E 218 ARG 0.004 0.001 ARG C 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13312.68 seconds wall clock time: 229 minutes 37.25 seconds (13777.25 seconds total)