Starting phenix.real_space_refine on Wed Feb 21 09:55:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy8_22524/02_2024/7jy8_22524_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy8_22524/02_2024/7jy8_22524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy8_22524/02_2024/7jy8_22524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy8_22524/02_2024/7jy8_22524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy8_22524/02_2024/7jy8_22524_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy8_22524/02_2024/7jy8_22524_trim_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 46728 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 64 5.49 5 Mg 9 5.21 5 S 116 5.16 5 C 14481 2.51 5 N 4017 2.21 5 O 4673 1.98 5 H 23368 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 31": "OE1" <-> "OE2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 94": "OD1" <-> "OD2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A ASP 110": "OD1" <-> "OD2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ASP 139": "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 233": "OE1" <-> "OE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ASP 161": "OD1" <-> "OD2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C ASP 110": "OD1" <-> "OD2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C GLU 325": "OE1" <-> "OE2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E GLU 31": "OE1" <-> "OE2" 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 ASP 110": "OD1" <-> "OD2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E ASP 139": "OD1" <-> "OD2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "E PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 233": "OE1" <-> "OE2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "E ASP 276": "OD1" <-> "OD2" Residue "E TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 296": "OE1" <-> "OE2" Residue "F GLU 4": "OE1" <-> "OE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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 233": "OE1" <-> "OE2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F GLU 281": "OE1" <-> "OE2" Residue "F GLU 285": "OE1" <-> "OE2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "G ASP 3": "OD1" <-> "OD2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G GLU 18": "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 GLU 158": "OE1" <-> "OE2" Residue "G TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 233": "OE1" <-> "OE2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G GLU 266": "OE1" <-> "OE2" Residue "G TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 3": "OD1" <-> "OD2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 100": "OD1" <-> "OD2" Residue "H ASP 110": "OD1" <-> "OD2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H GLU 154": "OE1" <-> "OE2" Residue "H GLU 156": "OE1" <-> "OE2" Residue "H GLU 158": "OE1" <-> "OE2" Residue "H PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 233": "OE1" <-> "OE2" Residue "H GLU 266": "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 314": "OE1" <-> "OE2" Residue "H GLU 325": "OE1" <-> "OE2" Residue "I GLU 38": "OE1" <-> "OE2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 100": "OD1" <-> "OD2" Residue "I ASP 110": "OD1" <-> "OD2" Residue "I GLU 154": "OE1" <-> "OE2" Residue "I GLU 156": "OE1" <-> "OE2" Residue "I GLU 158": "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 235": "OE1" <-> "OE2" Residue "I GLU 266": "OE1" <-> "OE2" Residue "I GLU 285": "OE1" <-> "OE2" Residue "I TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 296": "OE1" <-> "OE2" Residue "I GLU 314": "OE1" <-> "OE2" Residue "I GLU 325": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 46728 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: "T" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 320 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} 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: 15.14, per 1000 atoms: 0.32 Number of scatterers: 46728 At special positions: 0 Unit cell: (132.594, 121.814, 198.352, 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 64 15.00 Mg 9 11.99 O 4673 8.00 N 4017 7.00 C 14481 6.00 H 23368 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: 28.47 Conformation dependent library (CDL) restraints added in 3.9 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: 108 helices and 36 sheets defined 39.3% alpha, 19.3% beta 9 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 19.12 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 removed outlier: 3.654A 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: 3.630A pdb=" N GLU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 122 through 135 Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 166 through 185 removed outlier: 3.665A pdb=" N ARG A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLY A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 4.283A 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 Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 327 Processing helix chain 'B' and resid 2 through 21 removed outlier: 3.626A pdb=" N LYS B 6 " --> pdb=" O ILE B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' 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 86 removed outlier: 3.768A pdb=" N GLU B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 166 through 185 removed outlier: 3.514A pdb=" N ARG B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLY B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 270 through 280 Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 327 Processing helix chain 'C' and resid 3 through 21 removed outlier: 3.666A pdb=" N GLN C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS C 8 " --> pdb=" O GLU C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 45 through 51 Processing helix chain 'C' and resid 72 through 86 removed outlier: 3.647A pdb=" N GLU C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 107 Processing helix chain 'C' and resid 122 through 135 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 166 through 185 removed outlier: 3.531A pdb=" N ARG C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLY C 180 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 4.308A 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 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: 3.666A pdb=" N LYS D 6 " --> pdb=" O ILE D 2 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D 7 " --> pdb=" O ASP D 3 " (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 45 through 51 Processing helix chain 'D' and resid 72 through 86 removed outlier: 3.619A pdb=" N GLU D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 152 through 156 Processing helix chain 'D' and resid 166 through 185 removed outlier: 4.900A pdb=" N GLY D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 4.415A 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 removed outlier: 3.533A pdb=" N ASP D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) 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: 3.904A pdb=" N LYS E 6 " --> pdb=" O ILE E 2 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN E 7 " --> pdb=" O ASP E 3 " (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: 3.672A 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: 3.528A pdb=" N ARG E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLY E 180 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 4.319A 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 Processing helix chain 'E' and resid 302 through 311 Processing helix chain 'E' and resid 313 through 327 Processing helix chain 'F' and resid 2 through 21 removed outlier: 3.568A pdb=" N GLN F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 33 through 35 No H-bonds generated for 'chain 'F' and resid 33 through 35' Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 72 through 86 removed outlier: 3.706A pdb=" N GLU F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 107 Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 152 through 156 Processing helix chain 'F' and resid 166 through 185 removed outlier: 4.945A pdb=" N GLY F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 4.424A 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: 3.544A pdb=" N ASP F 276 " --> pdb=" O GLY F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 311 Processing helix chain 'F' and resid 313 through 327 Processing helix chain 'G' and resid 3 through 21 Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 33 through 35 No H-bonds generated for 'chain 'G' and resid 33 through 35' Processing helix chain 'G' and resid 45 through 51 Processing helix chain 'G' and resid 72 through 86 removed outlier: 3.789A pdb=" N GLU G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) 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: 3.570A pdb=" N ARG G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLY G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 4.280A 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 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 21 removed outlier: 3.623A pdb=" N LYS H 8 " --> pdb=" O GLU H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 51 Processing helix chain 'H' and resid 72 through 86 removed outlier: 3.743A pdb=" N GLU H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 107 Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 152 through 156 Processing helix chain 'H' and resid 166 through 185 removed outlier: 3.650A pdb=" N ARG H 176 " --> pdb=" O SER H 172 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY H 180 " --> pdb=" O ARG H 176 " (cutoff:3.500A) removed outlier: 4.165A 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 311 Processing helix chain 'H' and resid 313 through 327 Processing helix chain 'I' and resid 45 through 50 Processing helix chain 'I' and resid 72 through 86 removed outlier: 3.725A pdb=" N GLU I 86 " --> pdb=" O ALA I 82 " (cutoff:3.500A) 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: 3.743A pdb=" N ARG I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY I 180 " --> pdb=" O ARG I 176 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 218 Processing helix chain 'I' and resid 270 through 280 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: 6.460A pdb=" N ARG A 222 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 221 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 189 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE A 64 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE A 191 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N GLY A 66 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN A 193 " --> pdb=" O GLY A 66 " (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: 6.462A pdb=" N TYR A 293 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LYS A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 229 through 233 removed outlier: 6.737A pdb=" N GLU A 233 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 257 through 263 removed outlier: 6.282A pdb=" N ARG B 222 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B 221 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU B 189 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE B 64 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE B 191 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N GLY B 66 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN B 193 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 115 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 195 through 197 Processing sheet with id= G, first strand: chain 'B' and resid 285 through 287 removed outlier: 6.590A pdb=" N TYR B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LYS B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 229 through 233 removed outlier: 6.572A pdb=" N GLU B 233 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 257 through 263 removed outlier: 6.329A pdb=" N ARG C 222 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL C 221 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 189 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE C 64 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE C 191 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLY C 66 " --> pdb=" O PHE C 191 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN C 193 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.512A 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: 6.399A pdb=" N TYR C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.220A 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: 6.542A pdb=" N GLU C 233 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.216A 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: 6.292A pdb=" N ARG D 222 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL D 221 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 189 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE D 64 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE D 191 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N GLY D 66 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN D 193 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 6.559A 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 285 through 287 removed outlier: 6.439A pdb=" N TYR D 293 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 229 through 233 removed outlier: 6.541A pdb=" N GLU D 233 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 257 through 263 removed outlier: 6.229A pdb=" N ARG E 222 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL E 221 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU E 189 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE E 64 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE E 191 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N GLY E 66 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN E 193 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 6.552A 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 284 through 287 removed outlier: 6.392A pdb=" N TYR E 293 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LYS E 297 " --> pdb=" O TYR E 293 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 229 through 233 removed outlier: 6.534A pdb=" N GLU E 233 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.085A 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: 6.237A pdb=" N ARG F 222 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL F 221 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU F 189 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE F 64 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE F 191 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N GLY F 66 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASN F 193 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU F 115 " --> pdb=" O PHE F 92 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 195 through 197 Processing sheet with id= W, first strand: chain 'F' and resid 285 through 287 removed outlier: 6.461A pdb=" N TYR F 293 " --> pdb=" O LYS F 297 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS F 297 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 229 through 233 removed outlier: 3.524A pdb=" N GLY F 229 " --> pdb=" O GLU F 241 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU F 233 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL F 237 " --> pdb=" O GLU F 233 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 257 through 263 removed outlier: 6.262A pdb=" N ARG G 222 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL G 221 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU G 189 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ILE G 64 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE G 191 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N GLY G 66 " --> pdb=" O PHE G 191 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN G 193 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 6.578A 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 Processing sheet with id= AB, first strand: chain 'G' and resid 229 through 233 removed outlier: 6.436A pdb=" N GLU G 233 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 6.244A 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: 6.382A pdb=" N ARG H 222 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL H 221 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU H 189 " --> pdb=" O VAL H 62 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE H 64 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE H 191 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N GLY H 66 " --> pdb=" O PHE H 191 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN H 193 " --> pdb=" O GLY H 66 " (cutoff:3.500A) removed outlier: 6.625A 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 285 through 287 removed outlier: 6.430A pdb=" N TYR H 293 " --> pdb=" O LYS H 297 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LYS H 297 " --> pdb=" O TYR H 293 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 229 through 233 removed outlier: 6.463A pdb=" N GLU H 233 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL H 237 " --> pdb=" O GLU H 233 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 257 through 263 removed outlier: 6.396A pdb=" N ARG I 222 " --> pdb=" O VAL I 247 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL I 221 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU I 189 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE I 64 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE I 191 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLY I 66 " --> pdb=" O PHE I 191 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN I 193 " --> pdb=" O GLY I 66 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU I 115 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ASP I 94 " --> pdb=" O LEU I 115 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER I 117 " --> pdb=" O ASP I 94 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 195 through 197 Processing sheet with id= AI, first strand: chain 'I' and resid 285 through 287 removed outlier: 6.434A pdb=" N TYR I 293 " --> pdb=" O LYS I 297 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LYS I 297 " --> pdb=" O TYR I 293 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 229 through 233 removed outlier: 6.673A pdb=" N GLU I 233 " --> pdb=" O VAL I 237 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL I 237 " --> pdb=" O GLU I 233 " (cutoff:3.500A) 1007 hydrogen bonds defined for protein. 2946 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 16.03 Time building geometry restraints manager: 30.15 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: 23230 1.09 - 1.34: 7545 1.34 - 1.59: 16020 1.59 - 1.84: 274 1.84 - 2.08: 10 Bond restraints: 47079 Sorted by residual: bond pdb=" C4 AGS A 402 " pdb=" C5 AGS A 402 " ideal model delta sigma weight residual 1.386 1.477 -0.091 1.00e-02 1.00e+04 8.23e+01 bond pdb=" N3 DT S 6 " pdb=" H3 DT S 6 " 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 S 17 " pdb=" H3 DT S 17 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.14e+01 bond pdb=" N3 DT S 10 " pdb=" H3 DT S 10 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.13e+01 bond pdb=" N3 DT S 23 " pdb=" H3 DT S 23 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.13e+01 ... (remaining 47074 not shown) Histogram of bond angle deviations from ideal: 97.22 - 105.14: 747 105.14 - 113.06: 55855 113.06 - 120.98: 20860 120.98 - 128.90: 7958 128.90 - 136.82: 116 Bond angle restraints: 85536 Sorted by residual: angle pdb=" C5 AGS E 402 " pdb=" N7 AGS E 402 " pdb=" C8 AGS E 402 " ideal model delta sigma weight residual 103.67 108.41 -4.74 4.26e-01 5.51e+00 1.24e+02 angle pdb=" C5 AGS E 402 " pdb=" C4 AGS E 402 " pdb=" N3 AGS E 402 " ideal model delta sigma weight residual 126.80 118.56 8.24 7.41e-01 1.82e+00 1.24e+02 angle pdb=" C5 AGS A 402 " pdb=" C4 AGS A 402 " pdb=" N3 AGS A 402 " ideal model delta sigma weight residual 126.80 118.56 8.24 7.41e-01 1.82e+00 1.24e+02 angle pdb=" C5 AGS G 402 " pdb=" C4 AGS G 402 " pdb=" N3 AGS G 402 " ideal model delta sigma weight residual 126.80 118.88 7.92 7.41e-01 1.82e+00 1.14e+02 angle pdb=" C5 AGS G 402 " pdb=" N7 AGS G 402 " pdb=" C8 AGS G 402 " ideal model delta sigma weight residual 103.67 108.22 -4.55 4.26e-01 5.51e+00 1.14e+02 ... (remaining 85531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.33: 20212 32.33 - 64.66: 1363 64.66 - 96.99: 61 96.99 - 129.32: 7 129.32 - 161.65: 9 Dihedral angle restraints: 21652 sinusoidal: 12523 harmonic: 9129 Sorted by residual: dihedral pdb=" CA SER C 145 " pdb=" C SER C 145 " pdb=" N VAL C 146 " pdb=" CA VAL C 146 " ideal model delta harmonic sigma weight residual 180.00 146.16 33.84 0 5.00e+00 4.00e-02 4.58e+01 dihedral pdb=" CA SER H 145 " pdb=" C SER H 145 " pdb=" N VAL H 146 " pdb=" CA VAL H 146 " ideal model delta harmonic sigma weight residual 180.00 148.76 31.24 0 5.00e+00 4.00e-02 3.90e+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 180.00 149.64 30.36 0 5.00e+00 4.00e-02 3.69e+01 ... (remaining 21649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2445 0.093 - 0.186: 1117 0.186 - 0.280: 114 0.280 - 0.373: 13 0.373 - 0.466: 6 Chirality restraints: 3695 Sorted by residual: chirality pdb=" CA SER F 145 " pdb=" N SER F 145 " pdb=" C SER F 145 " pdb=" CB SER F 145 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.43e+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 2.08 0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" CA SER G 145 " pdb=" N SER G 145 " pdb=" C SER G 145 " pdb=" CB SER G 145 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 ... (remaining 3692 not shown) Planarity restraints: 6881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT S 8 " 0.012 2.00e-02 2.50e+03 2.75e-02 2.27e+01 pdb=" N1 DT S 8 " -0.056 2.00e-02 2.50e+03 pdb=" C2 DT S 8 " -0.008 2.00e-02 2.50e+03 pdb=" O2 DT S 8 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DT S 8 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT S 8 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT S 8 " 0.017 2.00e-02 2.50e+03 pdb=" C5 DT S 8 " -0.023 2.00e-02 2.50e+03 pdb=" C7 DT S 8 " -0.016 2.00e-02 2.50e+03 pdb=" C6 DT S 8 " -0.017 2.00e-02 2.50e+03 pdb=" H3 DT S 8 " 0.017 2.00e-02 2.50e+03 pdb=" H6 DT S 8 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 65 " -0.035 2.00e-02 2.50e+03 2.04e-02 1.25e+01 pdb=" CG TYR G 65 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR G 65 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR G 65 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR G 65 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR G 65 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR G 65 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR G 65 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 TYR G 65 " -0.024 2.00e-02 2.50e+03 pdb=" HD2 TYR G 65 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 TYR G 65 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR G 65 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 144 " -0.016 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C ASP G 144 " 0.061 2.00e-02 2.50e+03 pdb=" O ASP G 144 " -0.024 2.00e-02 2.50e+03 pdb=" N SER G 145 " -0.020 2.00e-02 2.50e+03 ... (remaining 6878 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.00: 492 2.00 - 2.65: 56312 2.65 - 3.30: 136277 3.30 - 3.95: 177796 3.95 - 4.60: 271090 Nonbonded interactions: 641967 Sorted by model distance: nonbonded pdb="HH11 ARG G 60 " pdb=" HG SER G 220 " model vdw 1.353 2.100 nonbonded pdb=" HH TYR D 293 " pdb=" HZ3 LYS D 322 " model vdw 1.354 2.100 nonbonded pdb="HH11 ARG F 60 " pdb=" HG SER F 220 " model vdw 1.408 2.100 nonbonded pdb="HH11 ARG B 60 " pdb=" HG SER B 220 " model vdw 1.416 2.100 nonbonded pdb="HH11 ARG D 60 " pdb=" HG SER D 220 " model vdw 1.422 2.100 ... (remaining 641962 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: 0.950 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: 0.520 Extract box with map and model: 5.520 Check model and map are aligned: 0.530 Set scattering table: 0.360 Process input model: 126.960 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.140 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:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 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 : 0.015 0.159 23711 Z= 0.942 Angle : 1.935 14.577 32133 Z= 1.408 Chirality : 0.096 0.466 3695 Planarity : 0.005 0.035 3997 Dihedral : 19.733 161.648 9132 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.12 % Favored : 96.71 % Rotamer: Outliers : 7.58 % Allowed : 9.21 % Favored : 83.20 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.00 (0.13), residues: 2946 helix: -1.58 (0.11), residues: 1250 sheet: 0.80 (0.22), residues: 461 loop : -1.79 (0.15), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 308 HIS 0.007 0.002 HIS F 97 PHE 0.023 0.004 PHE C 255 TYR 0.044 0.003 TYR G 65 ARG 0.012 0.001 ARG G 243 *********************** 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 592 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 415 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASP cc_start: 0.4056 (t0) cc_final: 0.3727 (m-30) REVERT: B 23 LYS cc_start: 0.6726 (tppt) cc_final: 0.6523 (tptp) REVERT: B 161 ASP cc_start: 0.5426 (m-30) cc_final: 0.5194 (t0) REVERT: B 171 MET cc_start: 0.8449 (mmm) cc_final: 0.8098 (mmp) REVERT: B 197 MET cc_start: 0.6833 (tpp) cc_final: 0.6535 (tpp) REVERT: B 293 TYR cc_start: 0.5480 (t80) cc_final: 0.4685 (t80) REVERT: C 5 ASN cc_start: 0.7091 (OUTLIER) cc_final: 0.6690 (m-40) REVERT: D 28 ARG cc_start: 0.8105 (mtt90) cc_final: 0.7760 (mmt180) REVERT: D 96 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7564 (mt-10) REVERT: D 105 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.7978 (ttm110) REVERT: D 146 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8515 (m) REVERT: D 205 ASN cc_start: 0.7284 (OUTLIER) cc_final: 0.6784 (p0) REVERT: F 27 MET cc_start: 0.8471 (ptt) cc_final: 0.8246 (ptt) REVERT: F 184 GLN cc_start: 0.7656 (mt0) cc_final: 0.7439 (mt0) REVERT: G 175 MET cc_start: 0.9110 (mmp) cc_final: 0.8851 (mmp) REVERT: H 170 MET cc_start: 0.8363 (ttp) cc_final: 0.8007 (ttp) REVERT: H 292 SER cc_start: 0.5027 (OUTLIER) cc_final: 0.4821 (m) REVERT: I 302 LYS cc_start: 0.3535 (OUTLIER) cc_final: 0.3255 (mttt) outliers start: 177 outliers final: 43 residues processed: 558 average time/residue: 2.3775 time to fit residues: 1523.0012 Evaluate side-chains 293 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 245 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 177 LYS Chi-restraints excluded: chain H residue 292 SER Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 315 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.9980 chunk 225 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 232 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 269 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN F 5 ASN F 236 ASN G 236 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23711 Z= 0.192 Angle : 0.609 7.023 32133 Z= 0.334 Chirality : 0.042 0.158 3695 Planarity : 0.003 0.030 3997 Dihedral : 17.528 177.452 3817 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.29 % Favored : 98.57 % Rotamer: Outliers : 3.60 % Allowed : 15.51 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 2946 helix: 0.84 (0.14), residues: 1267 sheet: 1.20 (0.22), residues: 504 loop : -1.97 (0.15), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 290 HIS 0.003 0.001 HIS I 163 PHE 0.013 0.001 PHE H 21 TYR 0.008 0.001 TYR F 65 ARG 0.003 0.001 ARG A 176 *********************** 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 341 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 257 time to evaluate : 2.882 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: A 144 ASP cc_start: 0.4381 (t0) cc_final: 0.4181 (t0) REVERT: A 156 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6032 (mp0) REVERT: B 123 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: B 161 ASP cc_start: 0.5669 (m-30) cc_final: 0.5299 (t0) REVERT: B 171 MET cc_start: 0.8477 (mmm) cc_final: 0.8130 (mmp) REVERT: B 317 LYS cc_start: 0.5150 (tppt) cc_final: 0.4863 (mttm) REVERT: C 277 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6953 (mm) REVERT: D 28 ARG cc_start: 0.8140 (mtt90) cc_final: 0.7801 (mmt180) REVERT: D 79 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8468 (m) REVERT: D 146 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.7970 (m) REVERT: F 27 MET cc_start: 0.8470 (ptp) cc_final: 0.8185 (ptt) REVERT: F 79 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8585 (m) REVERT: F 184 GLN cc_start: 0.7491 (mt0) cc_final: 0.7263 (mt0) REVERT: F 322 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6697 (mmmt) REVERT: H 170 MET cc_start: 0.8250 (ttp) cc_final: 0.7854 (ttp) REVERT: I 181 ASN cc_start: 0.4879 (OUTLIER) cc_final: 0.4228 (m110) REVERT: I 302 LYS cc_start: 0.3932 (OUTLIER) cc_final: 0.3417 (mttt) outliers start: 84 outliers final: 33 residues processed: 321 average time/residue: 2.3330 time to fit residues: 864.0252 Evaluate side-chains 272 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 230 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 322 LYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain H residue 177 LYS Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 236 ASN Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 315 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 270 optimal weight: 20.0000 chunk 291 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 267 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 257 GLN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN D 20 GLN E 124 GLN F 236 ASN F 312 ASN I 330 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23711 Z= 0.315 Angle : 0.658 9.776 32133 Z= 0.350 Chirality : 0.048 0.224 3695 Planarity : 0.004 0.049 3997 Dihedral : 17.113 178.946 3778 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.74 % Allowed : 17.40 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 2946 helix: 1.30 (0.14), residues: 1252 sheet: 1.14 (0.22), residues: 500 loop : -1.86 (0.15), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 290 HIS 0.004 0.001 HIS H 163 PHE 0.017 0.002 PHE E 191 TYR 0.024 0.002 TYR A 103 ARG 0.007 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 304 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 240 time to evaluate : 2.793 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: A 156 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6212 (mp0) REVERT: B 123 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6915 (mt-10) REVERT: B 161 ASP cc_start: 0.5962 (m-30) cc_final: 0.5444 (t0) REVERT: B 171 MET cc_start: 0.8455 (mmm) cc_final: 0.7990 (mmm) REVERT: D 28 ARG cc_start: 0.8356 (mtt90) cc_final: 0.7812 (mmt180) REVERT: F 16 GLN cc_start: 0.7937 (tp-100) cc_final: 0.7517 (tp-100) REVERT: F 79 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8624 (m) REVERT: F 184 GLN cc_start: 0.7546 (mt0) cc_final: 0.7319 (mt0) REVERT: F 322 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6662 (mmmt) REVERT: H 35 MET cc_start: 0.6180 (mmm) cc_final: 0.5564 (mtt) REVERT: H 170 MET cc_start: 0.8317 (ttp) cc_final: 0.7963 (ttp) REVERT: I 181 ASN cc_start: 0.4882 (OUTLIER) cc_final: 0.4290 (m110) outliers start: 64 outliers final: 40 residues processed: 291 average time/residue: 2.4962 time to fit residues: 843.3334 Evaluate side-chains 275 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 230 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 322 LYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 236 ASN Chi-restraints excluded: chain I residue 300 GLN Chi-restraints excluded: chain I residue 315 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 20.0000 chunk 203 optimal weight: 0.5980 chunk 140 optimal weight: 0.2980 chunk 29 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 181 optimal weight: 0.6980 chunk 271 optimal weight: 7.9990 chunk 287 optimal weight: 20.0000 chunk 141 optimal weight: 0.6980 chunk 256 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23711 Z= 0.154 Angle : 0.512 4.583 32133 Z= 0.281 Chirality : 0.042 0.146 3695 Planarity : 0.003 0.035 3997 Dihedral : 16.943 179.523 3767 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.31 % Allowed : 17.57 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 2946 helix: 1.86 (0.15), residues: 1268 sheet: 1.23 (0.22), residues: 500 loop : -1.75 (0.15), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 308 HIS 0.002 0.001 HIS H 163 PHE 0.010 0.001 PHE E 191 TYR 0.009 0.001 TYR C 291 ARG 0.002 0.000 ARG A 28 *********************** 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 298 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 244 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: B 123 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6931 (mt-10) REVERT: B 161 ASP cc_start: 0.5986 (m-30) cc_final: 0.5480 (t0) REVERT: B 171 MET cc_start: 0.8454 (mmm) cc_final: 0.8005 (mmp) REVERT: C 277 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7061 (mm) REVERT: D 28 ARG cc_start: 0.8322 (mtt90) cc_final: 0.7890 (mmt180) REVERT: D 79 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8435 (m) REVERT: F 184 GLN cc_start: 0.7448 (mt0) cc_final: 0.7225 (mt0) REVERT: F 322 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6691 (mmmt) REVERT: H 35 MET cc_start: 0.6209 (mmm) cc_final: 0.5632 (mtt) REVERT: H 170 MET cc_start: 0.8224 (ttp) cc_final: 0.7819 (ttp) REVERT: I 181 ASN cc_start: 0.4911 (OUTLIER) cc_final: 0.4328 (m110) outliers start: 54 outliers final: 29 residues processed: 288 average time/residue: 2.4197 time to fit residues: 800.7348 Evaluate side-chains 263 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 228 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 322 LYS Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 300 GLN Chi-restraints excluded: chain I residue 315 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 0.0870 chunk 162 optimal weight: 8.9990 chunk 4 optimal weight: 30.0000 chunk 213 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 244 optimal weight: 8.9990 chunk 198 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 146 optimal weight: 0.9990 chunk 257 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23711 Z= 0.199 Angle : 0.538 7.294 32133 Z= 0.289 Chirality : 0.043 0.154 3695 Planarity : 0.003 0.036 3997 Dihedral : 16.696 179.411 3757 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.14 % Allowed : 17.48 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 2946 helix: 1.96 (0.15), residues: 1268 sheet: 1.21 (0.22), residues: 500 loop : -1.66 (0.15), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 290 HIS 0.002 0.001 HIS D 163 PHE 0.015 0.001 PHE E 191 TYR 0.013 0.001 TYR C 291 ARG 0.003 0.000 ARG F 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 287 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 237 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6220 (mp0) REVERT: A 197 MET cc_start: 0.3814 (pmt) cc_final: 0.3494 (pmt) REVERT: A 208 THR cc_start: 0.4882 (OUTLIER) cc_final: 0.4552 (m) REVERT: B 123 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: B 161 ASP cc_start: 0.6062 (m-30) cc_final: 0.5501 (t0) REVERT: B 171 MET cc_start: 0.8391 (mmm) cc_final: 0.8040 (mmp) REVERT: C 5 ASN cc_start: 0.6889 (m-40) cc_final: 0.6423 (m-40) REVERT: D 28 ARG cc_start: 0.8331 (mtt90) cc_final: 0.7907 (mmt180) REVERT: D 79 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8491 (m) REVERT: E 145 SER cc_start: 0.6554 (OUTLIER) cc_final: 0.6326 (t) REVERT: F 16 GLN cc_start: 0.7727 (tp-100) cc_final: 0.7291 (tp-100) REVERT: F 184 GLN cc_start: 0.7469 (mt0) cc_final: 0.7256 (mt0) REVERT: F 322 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6549 (mmmt) REVERT: H 35 MET cc_start: 0.6237 (mmm) cc_final: 0.5675 (mtt) REVERT: H 169 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7274 (mtp180) REVERT: H 170 MET cc_start: 0.8248 (ttp) cc_final: 0.7904 (ttp) REVERT: I 181 ASN cc_start: 0.4851 (OUTLIER) cc_final: 0.4366 (m-40) REVERT: I 215 LEU cc_start: 0.6137 (tp) cc_final: 0.5771 (mm) REVERT: I 222 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.5532 (mtp85) outliers start: 50 outliers final: 27 residues processed: 281 average time/residue: 2.4501 time to fit residues: 791.1777 Evaluate side-chains 269 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 233 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 322 LYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 169 ARG Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 222 ARG Chi-restraints excluded: chain I residue 315 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 287 optimal weight: 20.0000 chunk 238 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN H 257 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23711 Z= 0.314 Angle : 0.623 10.210 32133 Z= 0.330 Chirality : 0.046 0.207 3695 Planarity : 0.004 0.045 3997 Dihedral : 16.608 178.431 3748 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.40 % Allowed : 16.80 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 2946 helix: 1.40 (0.14), residues: 1325 sheet: 1.12 (0.22), residues: 500 loop : -1.60 (0.15), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 290 HIS 0.004 0.001 HIS H 163 PHE 0.016 0.002 PHE C 217 TYR 0.010 0.002 TYR B 65 ARG 0.005 0.001 ARG E 196 *********************** 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 283 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 227 time to evaluate : 2.795 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 156 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6127 (mp0) REVERT: A 197 MET cc_start: 0.3759 (pmt) cc_final: 0.3474 (pmt) REVERT: A 208 THR cc_start: 0.4905 (OUTLIER) cc_final: 0.4548 (m) REVERT: B 123 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6921 (mt-10) REVERT: B 152 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7230 (ttmt) REVERT: B 161 ASP cc_start: 0.6095 (m-30) cc_final: 0.5452 (t0) REVERT: B 171 MET cc_start: 0.8381 (mmm) cc_final: 0.7973 (mmp) REVERT: D 28 ARG cc_start: 0.8331 (mtt90) cc_final: 0.7949 (mmt180) REVERT: E 145 SER cc_start: 0.7082 (OUTLIER) cc_final: 0.6740 (t) REVERT: H 35 MET cc_start: 0.6406 (mmm) cc_final: 0.5903 (mtt) REVERT: H 169 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7302 (mtp180) REVERT: H 170 MET cc_start: 0.8291 (ttp) cc_final: 0.7961 (ttp) REVERT: I 181 ASN cc_start: 0.4879 (OUTLIER) cc_final: 0.4389 (m-40) REVERT: I 226 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6672 (mtt-85) outliers start: 56 outliers final: 35 residues processed: 273 average time/residue: 2.4875 time to fit residues: 789.5231 Evaluate side-chains 263 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 220 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 322 LYS Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 169 ARG Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 226 ARG Chi-restraints excluded: chain I residue 315 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 163 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 241 optimal weight: 0.0980 chunk 160 optimal weight: 8.9990 chunk 286 optimal weight: 8.9990 chunk 179 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN F 184 GLN I 300 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23711 Z= 0.185 Angle : 0.521 6.031 32133 Z= 0.283 Chirality : 0.043 0.141 3695 Planarity : 0.003 0.040 3997 Dihedral : 16.521 179.643 3744 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.63 % Allowed : 17.78 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 2946 helix: 1.61 (0.15), residues: 1340 sheet: 1.17 (0.22), residues: 500 loop : -1.54 (0.16), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 308 HIS 0.002 0.001 HIS H 163 PHE 0.014 0.001 PHE E 191 TYR 0.009 0.001 TYR A 103 ARG 0.002 0.000 ARG E 196 *********************** 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 267 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 229 time to evaluate : 2.853 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 197 MET cc_start: 0.3731 (pmt) cc_final: 0.3442 (pmt) REVERT: B 123 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6883 (mt-10) REVERT: B 161 ASP cc_start: 0.6211 (m-30) cc_final: 0.5595 (t0) REVERT: B 171 MET cc_start: 0.8359 (mmm) cc_final: 0.7949 (mmp) REVERT: D 28 ARG cc_start: 0.8318 (mtt90) cc_final: 0.7875 (mmt180) REVERT: E 145 SER cc_start: 0.6662 (OUTLIER) cc_final: 0.6443 (t) REVERT: F 322 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6792 (mmmm) REVERT: H 35 MET cc_start: 0.6346 (mmm) cc_final: 0.5883 (mtt) REVERT: H 170 MET cc_start: 0.8241 (ttp) cc_final: 0.7841 (ttp) REVERT: I 175 MET cc_start: 0.5364 (mmm) cc_final: 0.5139 (mmm) REVERT: I 181 ASN cc_start: 0.4849 (OUTLIER) cc_final: 0.4378 (m-40) outliers start: 38 outliers final: 28 residues processed: 262 average time/residue: 2.4061 time to fit residues: 727.1611 Evaluate side-chains 249 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 217 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 322 LYS Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 315 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 170 optimal weight: 0.0980 chunk 86 optimal weight: 0.0570 chunk 56 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 141 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN B 194 GLN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23711 Z= 0.136 Angle : 0.466 6.552 32133 Z= 0.256 Chirality : 0.041 0.147 3695 Planarity : 0.003 0.034 3997 Dihedral : 16.242 179.835 3744 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.37 % Allowed : 18.12 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.15), residues: 2946 helix: 2.02 (0.15), residues: 1340 sheet: 1.28 (0.22), residues: 500 loop : -1.37 (0.16), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 308 HIS 0.003 0.001 HIS C 97 PHE 0.016 0.001 PHE I 191 TYR 0.015 0.001 TYR C 291 ARG 0.002 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 262 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 230 time to evaluate : 2.816 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 156 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6146 (mp0) REVERT: B 161 ASP cc_start: 0.6116 (m-30) cc_final: 0.5513 (t0) REVERT: B 171 MET cc_start: 0.8339 (mmm) cc_final: 0.7924 (mmp) REVERT: C 7 GLN cc_start: 0.7088 (mt0) cc_final: 0.6836 (mt0) REVERT: D 28 ARG cc_start: 0.8250 (mtt90) cc_final: 0.7889 (mmt180) REVERT: E 145 SER cc_start: 0.6386 (OUTLIER) cc_final: 0.6165 (t) REVERT: F 208 THR cc_start: 0.8885 (p) cc_final: 0.8639 (t) REVERT: F 322 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6740 (mmmm) REVERT: H 35 MET cc_start: 0.6222 (mmm) cc_final: 0.5776 (mtt) REVERT: H 170 MET cc_start: 0.8175 (ttp) cc_final: 0.7829 (ttp) REVERT: I 181 ASN cc_start: 0.4838 (OUTLIER) cc_final: 0.4383 (m-40) REVERT: I 202 MET cc_start: 0.2068 (OUTLIER) cc_final: 0.1600 (ttt) outliers start: 32 outliers final: 16 residues processed: 258 average time/residue: 2.4585 time to fit residues: 729.3530 Evaluate side-chains 242 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 221 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 322 LYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 222 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 5.9990 chunk 274 optimal weight: 20.0000 chunk 250 optimal weight: 0.9980 chunk 266 optimal weight: 30.0000 chunk 160 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 241 optimal weight: 0.6980 chunk 252 optimal weight: 0.9990 chunk 265 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN E 7 GLN E 236 ASN F 184 GLN G 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23711 Z= 0.162 Angle : 0.492 6.435 32133 Z= 0.266 Chirality : 0.042 0.171 3695 Planarity : 0.003 0.037 3997 Dihedral : 16.146 179.855 3739 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.07 % Allowed : 18.47 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.15), residues: 2946 helix: 2.03 (0.15), residues: 1340 sheet: 1.32 (0.22), residues: 500 loop : -1.32 (0.16), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 308 HIS 0.002 0.001 HIS D 163 PHE 0.014 0.001 PHE I 255 TYR 0.011 0.001 TYR I 65 ARG 0.003 0.000 ARG F 196 *********************** 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 245 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 2.738 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 156 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6071 (mp0) REVERT: B 161 ASP cc_start: 0.6152 (m-30) cc_final: 0.5531 (t0) REVERT: B 171 MET cc_start: 0.8350 (mmm) cc_final: 0.7938 (mmp) REVERT: C 7 GLN cc_start: 0.7091 (mt0) cc_final: 0.6849 (mt0) REVERT: D 28 ARG cc_start: 0.8284 (mtt90) cc_final: 0.7911 (mmt180) REVERT: F 208 THR cc_start: 0.8917 (p) cc_final: 0.8620 (t) REVERT: F 322 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6690 (mmmm) REVERT: H 35 MET cc_start: 0.6238 (mmm) cc_final: 0.5803 (mtt) REVERT: H 170 MET cc_start: 0.8191 (ttp) cc_final: 0.7825 (ttp) REVERT: I 181 ASN cc_start: 0.4832 (OUTLIER) cc_final: 0.4390 (m-40) outliers start: 25 outliers final: 19 residues processed: 243 average time/residue: 2.4579 time to fit residues: 686.2521 Evaluate side-chains 238 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 216 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 322 LYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 222 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.0470 chunk 282 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 272 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN E 236 ASN F 184 GLN G 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23711 Z= 0.201 Angle : 0.519 7.368 32133 Z= 0.279 Chirality : 0.043 0.177 3695 Planarity : 0.003 0.037 3997 Dihedral : 16.143 179.918 3739 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.03 % Allowed : 18.25 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.15), residues: 2946 helix: 1.95 (0.15), residues: 1341 sheet: 1.34 (0.22), residues: 499 loop : -1.32 (0.16), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 308 HIS 0.003 0.001 HIS H 163 PHE 0.015 0.001 PHE E 191 TYR 0.012 0.001 TYR I 65 ARG 0.003 0.000 ARG E 196 ********************** 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 245 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 221 time to evaluate : 3.203 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: A 156 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6204 (mp0) REVERT: B 171 MET cc_start: 0.8360 (mmm) cc_final: 0.7948 (mmp) REVERT: C 7 GLN cc_start: 0.7133 (mt0) cc_final: 0.6897 (mt0) REVERT: D 28 ARG cc_start: 0.8288 (mtt90) cc_final: 0.7893 (mmt180) REVERT: F 322 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6560 (mmmm) REVERT: H 35 MET cc_start: 0.6345 (mmm) cc_final: 0.5834 (mtt) REVERT: H 170 MET cc_start: 0.8212 (ttp) cc_final: 0.7855 (ttp) REVERT: I 181 ASN cc_start: 0.4823 (OUTLIER) cc_final: 0.4387 (m-40) outliers start: 24 outliers final: 18 residues processed: 243 average time/residue: 2.5119 time to fit residues: 701.7670 Evaluate side-chains 236 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 215 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 322 LYS Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 2.9990 chunk 250 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 242 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN E 7 GLN E 236 ASN F 184 GLN G 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.217423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.166127 restraints weight = 64629.866| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.16 r_work: 0.3090 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23711 Z= 0.195 Angle : 0.513 7.117 32133 Z= 0.276 Chirality : 0.042 0.182 3695 Planarity : 0.003 0.039 3997 Dihedral : 16.122 179.992 3738 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.11 % Allowed : 18.29 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.15), residues: 2946 helix: 1.92 (0.15), residues: 1341 sheet: 1.34 (0.22), residues: 499 loop : -1.31 (0.16), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 308 HIS 0.003 0.001 HIS B 163 PHE 0.018 0.002 PHE I 255 TYR 0.012 0.001 TYR C 291 ARG 0.003 0.000 ARG E 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14093.43 seconds wall clock time: 243 minutes 8.23 seconds (14588.23 seconds total)