Starting phenix.real_space_refine on Thu Nov 16 22:49:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bki_9405/11_2023/5bki_9405_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bki_9405/11_2023/5bki_9405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bki_9405/11_2023/5bki_9405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bki_9405/11_2023/5bki_9405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bki_9405/11_2023/5bki_9405_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bki_9405/11_2023/5bki_9405_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Cd 12 9.23 5 K 5 8.98 5 S 68 5.16 5 C 10688 2.51 5 N 2896 2.21 5 O 3264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A ASP 64": "OD1" <-> "OD2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 245": "OD1" <-> "OD2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C ASP 64": "OD1" <-> "OD2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 245": "OD1" <-> "OD2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C ASP 284": "OD1" <-> "OD2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E ASP 64": "OD1" <-> "OD2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E ASP 202": "OD1" <-> "OD2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 245": "OD1" <-> "OD2" Residue "E ASP 254": "OD1" <-> "OD2" Residue "E GLU 266": "OE1" <-> "OE2" Residue "E ASP 284": "OD1" <-> "OD2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G ASP 64": "OD1" <-> "OD2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G ASP 202": "OD1" <-> "OD2" Residue "G ARG 213": "NH1" <-> "NH2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 245": "OD1" <-> "OD2" Residue "G ASP 254": "OD1" <-> "OD2" Residue "G GLU 266": "OE1" <-> "OE2" Residue "G ASP 284": "OD1" <-> "OD2" Residue "G ASP 305": "OD1" <-> "OD2" Residue "G PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B ASP 245": "OD1" <-> "OD2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B ASP 309": "OD1" <-> "OD2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 145": "OD1" <-> "OD2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D ASP 245": "OD1" <-> "OD2" Residue "D TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "D ASP 309": "OD1" <-> "OD2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 328": "OE1" <-> "OE2" Residue "F PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 145": "OD1" <-> "OD2" Residue "F ASP 169": "OD1" <-> "OD2" Residue "F ASP 184": "OD1" <-> "OD2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F ASP 244": "OD1" <-> "OD2" Residue "F ASP 245": "OD1" <-> "OD2" Residue "F TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 254": "OD1" <-> "OD2" Residue "F ARG 263": "NH1" <-> "NH2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F ASP 300": "OD1" <-> "OD2" Residue "F ASP 309": "OD1" <-> "OD2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "H PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 145": "OD1" <-> "OD2" Residue "H ASP 169": "OD1" <-> "OD2" Residue "H ASP 184": "OD1" <-> "OD2" Residue "H ARG 199": "NH1" <-> "NH2" Residue "H ASP 244": "OD1" <-> "OD2" Residue "H ASP 245": "OD1" <-> "OD2" Residue "H TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 254": "OD1" <-> "OD2" Residue "H ARG 263": "NH1" <-> "NH2" Residue "H GLU 271": "OE1" <-> "OE2" Residue "H ASP 300": "OD1" <-> "OD2" Residue "H ASP 309": "OD1" <-> "OD2" Residue "H TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 328": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 16933 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "E" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "G" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "B" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "D" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "F" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "H" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 41 Ad-hoc single atom residues: {' CD': 1} Unusual residues: {' K': 5, 'PGW': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Ad-hoc single atom residues: {' CD': 1} Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Ad-hoc single atom residues: {' CD': 1} Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Ad-hoc single atom residues: {' CD': 1} Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CD': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CD': 2} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CD': 2} Chain breaks: 2 Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CD': 2} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.32, per 1000 atoms: 0.55 Number of scatterers: 16933 At special positions: 0 Unit cell: (152.358, 152.358, 117.283, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cd 12 47.96 K 5 19.00 S 68 16.00 O 3264 8.00 N 2896 7.00 C 10688 6.00 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: 6.35 Conformation dependent library (CDL) restraints added in 3.0 seconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 16 sheets defined 41.4% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 22 through 42 removed outlier: 3.619A pdb=" N ALA A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 70 through 104 removed outlier: 3.636A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 128 No H-bonds generated for 'chain 'A' and resid 125 through 128' Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 167 through 170 No H-bonds generated for 'chain 'A' and resid 167 through 170' Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 188 through 201 removed outlier: 3.652A pdb=" N LYS A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 removed outlier: 3.551A pdb=" N ILE A 217 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU A 218 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN A 219 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 220 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET A 222 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 223 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 240 removed outlier: 3.570A pdb=" N SER A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 280 through 283 No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.047A pdb=" N GLU A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 42 removed outlier: 3.618A pdb=" N ALA C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 57 Processing helix chain 'C' and resid 70 through 104 removed outlier: 3.636A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 91 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 128 No H-bonds generated for 'chain 'C' and resid 125 through 128' Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 167 through 170 No H-bonds generated for 'chain 'C' and resid 167 through 170' Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 188 through 201 removed outlier: 3.652A pdb=" N LYS C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 223 removed outlier: 3.551A pdb=" N ILE C 217 " --> pdb=" O TYR C 214 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU C 218 " --> pdb=" O GLU C 215 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN C 219 " --> pdb=" O ASN C 216 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 220 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET C 222 " --> pdb=" O GLN C 219 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA C 223 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 240 removed outlier: 3.571A pdb=" N SER C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 255 Processing helix chain 'C' and resid 280 through 283 No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 285 through 289 Processing helix chain 'C' and resid 324 through 331 removed outlier: 4.047A pdb=" N GLU C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 42 removed outlier: 3.619A pdb=" N ALA E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 70 through 104 removed outlier: 3.635A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR E 78 " --> pdb=" O TYR E 74 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 128 No H-bonds generated for 'chain 'E' and resid 125 through 128' Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 167 through 170 No H-bonds generated for 'chain 'E' and resid 167 through 170' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 188 through 201 removed outlier: 3.653A pdb=" N LYS E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 223 removed outlier: 3.551A pdb=" N ILE E 217 " --> pdb=" O TYR E 214 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU E 218 " --> pdb=" O GLU E 215 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN E 219 " --> pdb=" O ASN E 216 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 220 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET E 222 " --> pdb=" O GLN E 219 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA E 223 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 240 removed outlier: 3.570A pdb=" N SER E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 255 Processing helix chain 'E' and resid 280 through 283 No H-bonds generated for 'chain 'E' and resid 280 through 283' Processing helix chain 'E' and resid 285 through 289 Processing helix chain 'E' and resid 324 through 331 removed outlier: 4.048A pdb=" N GLU E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG E 329 " --> pdb=" O GLU E 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 42 removed outlier: 3.618A pdb=" N ALA G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 57 Processing helix chain 'G' and resid 70 through 104 removed outlier: 3.635A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR G 78 " --> pdb=" O TYR G 74 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL G 91 " --> pdb=" O PHE G 87 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 128 No H-bonds generated for 'chain 'G' and resid 125 through 128' Processing helix chain 'G' and resid 147 through 155 Processing helix chain 'G' and resid 167 through 170 No H-bonds generated for 'chain 'G' and resid 167 through 170' Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 188 through 201 removed outlier: 3.652A pdb=" N LYS G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 223 removed outlier: 3.550A pdb=" N ILE G 217 " --> pdb=" O TYR G 214 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU G 218 " --> pdb=" O GLU G 215 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN G 219 " --> pdb=" O ASN G 216 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU G 220 " --> pdb=" O ILE G 217 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET G 222 " --> pdb=" O GLN G 219 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA G 223 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 240 removed outlier: 3.570A pdb=" N SER G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 255 Processing helix chain 'G' and resid 280 through 283 No H-bonds generated for 'chain 'G' and resid 280 through 283' Processing helix chain 'G' and resid 285 through 289 Processing helix chain 'G' and resid 324 through 331 removed outlier: 4.048A pdb=" N GLU G 328 " --> pdb=" O PRO G 324 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 removed outlier: 3.847A pdb=" N ARG B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 154 Processing helix chain 'B' and resid 167 through 170 No H-bonds generated for 'chain 'B' and resid 167 through 170' Processing helix chain 'B' and resid 188 through 201 removed outlier: 3.525A pdb=" N GLY B 197 " --> pdb=" O HIS B 193 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 223 removed outlier: 3.534A pdb=" N ARG B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 239 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 280 through 283 No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 285 through 288 No H-bonds generated for 'chain 'B' and resid 285 through 288' Processing helix chain 'B' and resid 324 through 333 removed outlier: 3.952A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 133 removed outlier: 3.847A pdb=" N ARG D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 154 Processing helix chain 'D' and resid 167 through 170 No H-bonds generated for 'chain 'D' and resid 167 through 170' Processing helix chain 'D' and resid 188 through 201 removed outlier: 3.525A pdb=" N GLY D 197 " --> pdb=" O HIS D 193 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 223 removed outlier: 3.534A pdb=" N ARG D 221 " --> pdb=" O ILE D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 239 Processing helix chain 'D' and resid 248 through 255 Processing helix chain 'D' and resid 280 through 283 No H-bonds generated for 'chain 'D' and resid 280 through 283' Processing helix chain 'D' and resid 285 through 288 No H-bonds generated for 'chain 'D' and resid 285 through 288' Processing helix chain 'D' and resid 324 through 333 removed outlier: 3.953A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 133 removed outlier: 3.847A pdb=" N ARG F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU F 133 " --> pdb=" O GLU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 154 Processing helix chain 'F' and resid 167 through 170 No H-bonds generated for 'chain 'F' and resid 167 through 170' Processing helix chain 'F' and resid 188 through 201 removed outlier: 3.525A pdb=" N GLY F 197 " --> pdb=" O HIS F 193 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 223 removed outlier: 3.534A pdb=" N ARG F 221 " --> pdb=" O ILE F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 239 Processing helix chain 'F' and resid 248 through 255 Processing helix chain 'F' and resid 280 through 283 No H-bonds generated for 'chain 'F' and resid 280 through 283' Processing helix chain 'F' and resid 285 through 288 No H-bonds generated for 'chain 'F' and resid 285 through 288' Processing helix chain 'F' and resid 324 through 333 removed outlier: 3.951A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 133 removed outlier: 3.847A pdb=" N ARG H 132 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU H 133 " --> pdb=" O GLU H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 154 Processing helix chain 'H' and resid 167 through 170 No H-bonds generated for 'chain 'H' and resid 167 through 170' Processing helix chain 'H' and resid 188 through 201 removed outlier: 3.525A pdb=" N GLY H 197 " --> pdb=" O HIS H 193 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS H 200 " --> pdb=" O LEU H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 223 removed outlier: 3.534A pdb=" N ARG H 221 " --> pdb=" O ILE H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 239 Processing helix chain 'H' and resid 248 through 255 Processing helix chain 'H' and resid 280 through 283 No H-bonds generated for 'chain 'H' and resid 280 through 283' Processing helix chain 'H' and resid 285 through 288 No H-bonds generated for 'chain 'H' and resid 285 through 288' Processing helix chain 'H' and resid 324 through 333 removed outlier: 3.952A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.329A pdb=" N VAL A 118 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A 120 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL A 119 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 181 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N CYS A 121 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL A 183 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG A 206 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL A 183 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 208 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN A 227 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA A 211 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 229 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 262 through 268 removed outlier: 6.884A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.329A pdb=" N VAL C 118 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU C 142 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 120 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL C 119 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL C 181 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N CYS C 121 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL C 183 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG C 206 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL C 183 " --> pdb=" O ARG C 206 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE C 208 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLN C 227 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA C 211 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE C 229 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 262 through 268 removed outlier: 6.884A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 158 through 161 removed outlier: 6.330A pdb=" N VAL E 118 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU E 142 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE E 120 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL E 119 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL E 181 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N CYS E 121 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL E 183 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG E 206 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL E 183 " --> pdb=" O ARG E 206 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE E 208 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN E 227 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA E 211 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE E 229 " --> pdb=" O ALA E 211 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 262 through 268 removed outlier: 6.884A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 158 through 161 removed outlier: 6.330A pdb=" N VAL G 118 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU G 142 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE G 120 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL G 119 " --> pdb=" O ARG G 179 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL G 181 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N CYS G 121 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL G 183 " --> pdb=" O CYS G 121 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG G 206 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL G 183 " --> pdb=" O ARG G 206 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE G 208 " --> pdb=" O VAL G 183 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN G 227 " --> pdb=" O ALA G 209 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA G 211 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE G 229 " --> pdb=" O ALA G 211 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 262 through 268 removed outlier: 6.885A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 227 through 230 removed outlier: 6.583A pdb=" N VAL B 181 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLU B 210 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL B 183 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN B 158 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ALA B 143 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL B 160 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 262 through 268 removed outlier: 6.991A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 227 through 230 removed outlier: 6.582A pdb=" N VAL D 181 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLU D 210 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL D 183 " --> pdb=" O GLU D 210 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN D 158 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ALA D 143 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL D 160 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 262 through 268 removed outlier: 6.991A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 227 through 230 removed outlier: 6.582A pdb=" N VAL F 181 " --> pdb=" O ILE F 208 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLU F 210 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL F 183 " --> pdb=" O GLU F 210 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN F 158 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA F 143 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL F 160 " --> pdb=" O ALA F 143 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 262 through 268 removed outlier: 6.991A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 227 through 230 removed outlier: 6.581A pdb=" N VAL H 181 " --> pdb=" O ILE H 208 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLU H 210 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL H 183 " --> pdb=" O GLU H 210 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN H 158 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ALA H 143 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL H 160 " --> pdb=" O ALA H 143 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 262 through 268 removed outlier: 6.991A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.12 Time building geometry restraints manager: 6.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2961 1.31 - 1.43: 4079 1.43 - 1.56: 9978 1.56 - 1.68: 18 1.68 - 1.81: 112 Bond restraints: 17148 Sorted by residual: bond pdb=" C10 PGW C 402 " pdb=" C9 PGW C 402 " ideal model delta sigma weight residual 1.333 1.536 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C10 PGW E 402 " pdb=" C9 PGW E 402 " ideal model delta sigma weight residual 1.333 1.536 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C10 PGW G 402 " pdb=" C9 PGW G 402 " ideal model delta sigma weight residual 1.333 1.536 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C10 PGW A 402 " pdb=" C9 PGW A 402 " ideal model delta sigma weight residual 1.333 1.535 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C1 PGW E 402 " pdb=" O01 PGW E 402 " ideal model delta sigma weight residual 1.332 1.433 -0.101 2.00e-02 2.50e+03 2.54e+01 ... (remaining 17143 not shown) Histogram of bond angle deviations from ideal: 80.95 - 91.56: 4 91.56 - 102.18: 44 102.18 - 112.79: 9451 112.79 - 123.40: 13031 123.40 - 134.01: 626 Bond angle restraints: 23156 Sorted by residual: angle pdb=" C06 PGW C 402 " pdb=" C07 PGW C 402 " pdb=" C08 PGW C 402 " ideal model delta sigma weight residual 112.92 80.95 31.97 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C06 PGW A 402 " pdb=" C07 PGW A 402 " pdb=" C08 PGW A 402 " ideal model delta sigma weight residual 112.92 80.96 31.96 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C06 PGW G 402 " pdb=" C07 PGW G 402 " pdb=" C08 PGW G 402 " ideal model delta sigma weight residual 112.92 80.96 31.96 3.00e+00 1.11e-01 1.13e+02 angle pdb=" C06 PGW E 402 " pdb=" C07 PGW E 402 " pdb=" C08 PGW E 402 " ideal model delta sigma weight residual 112.92 80.96 31.96 3.00e+00 1.11e-01 1.13e+02 angle pdb=" N PHE E 38 " pdb=" CA PHE E 38 " pdb=" C PHE E 38 " ideal model delta sigma weight residual 111.36 119.29 -7.93 1.09e+00 8.42e-01 5.30e+01 ... (remaining 23151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.30: 9740 23.30 - 46.59: 584 46.59 - 69.89: 96 69.89 - 93.18: 8 93.18 - 116.48: 8 Dihedral angle restraints: 10436 sinusoidal: 4284 harmonic: 6152 Sorted by residual: dihedral pdb=" CA GLY G 108 " pdb=" C GLY G 108 " pdb=" N LEU G 109 " pdb=" CA LEU G 109 " ideal model delta harmonic sigma weight residual 180.00 154.74 25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA GLY E 108 " pdb=" C GLY E 108 " pdb=" N LEU E 109 " pdb=" CA LEU E 109 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA GLY A 108 " pdb=" C GLY A 108 " pdb=" N LEU A 109 " pdb=" CA LEU A 109 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 10433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1680 0.052 - 0.104: 789 0.104 - 0.156: 195 0.156 - 0.208: 8 0.208 - 0.259: 20 Chirality restraints: 2692 Sorted by residual: chirality pdb=" CA PHE C 38 " pdb=" N PHE C 38 " pdb=" C PHE C 38 " pdb=" CB PHE C 38 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA PHE E 38 " pdb=" N PHE E 38 " pdb=" C PHE E 38 " pdb=" CB PHE E 38 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA PHE A 38 " pdb=" N PHE A 38 " pdb=" C PHE A 38 " pdb=" CB PHE A 38 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 2689 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW C 402 " -0.306 2.00e-02 2.50e+03 3.09e-01 9.52e+02 pdb=" C10 PGW C 402 " 0.307 2.00e-02 2.50e+03 pdb=" C8 PGW C 402 " -0.311 2.00e-02 2.50e+03 pdb=" C9 PGW C 402 " 0.310 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW E 402 " -0.306 2.00e-02 2.50e+03 3.09e-01 9.52e+02 pdb=" C10 PGW E 402 " 0.307 2.00e-02 2.50e+03 pdb=" C8 PGW E 402 " -0.311 2.00e-02 2.50e+03 pdb=" C9 PGW E 402 " 0.310 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 402 " 0.306 2.00e-02 2.50e+03 3.08e-01 9.52e+02 pdb=" C10 PGW A 402 " -0.307 2.00e-02 2.50e+03 pdb=" C8 PGW A 402 " 0.311 2.00e-02 2.50e+03 pdb=" C9 PGW A 402 " -0.310 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 5265 2.83 - 3.41: 16672 3.41 - 3.98: 30329 3.98 - 4.56: 43752 4.56 - 5.14: 66930 Nonbonded interactions: 162948 Sorted by model distance: nonbonded pdb=" O PHE E 75 " pdb=" CG2 THR E 78 " model vdw 2.252 3.460 nonbonded pdb=" O PHE C 75 " pdb=" CG2 THR C 78 " model vdw 2.252 3.460 nonbonded pdb=" O PHE A 75 " pdb=" CG2 THR A 78 " model vdw 2.253 3.460 nonbonded pdb=" O PHE G 75 " pdb=" CG2 THR G 78 " model vdw 2.253 3.460 nonbonded pdb=" OG SER A 124 " pdb=" OD2 ASP A 184 " model vdw 2.254 2.440 ... (remaining 162943 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 20 through 336 or resid 401 through 402)) selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.400 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 46.210 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.010 0.203 17148 Z= 0.660 Angle : 1.043 31.969 23156 Z= 0.541 Chirality : 0.060 0.259 2692 Planarity : 0.012 0.309 3000 Dihedral : 15.270 116.480 6484 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.44 % Allowed : 6.54 % Favored : 93.03 % 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: -5.10 (0.13), residues: 2140 helix: -4.22 (0.08), residues: 1060 sheet: -0.47 (0.26), residues: 356 loop : -3.22 (0.17), residues: 724 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 433 time to evaluate : 2.107 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 437 average time/residue: 0.3538 time to fit residues: 219.9289 Evaluate side-chains 368 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 364 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1492 time to fit residues: 3.7372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 108 optimal weight: 0.5980 chunk 85 optimal weight: 0.2980 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17148 Z= 0.203 Angle : 0.491 4.686 23156 Z= 0.268 Chirality : 0.046 0.138 2692 Planarity : 0.004 0.029 3000 Dihedral : 8.723 81.119 2480 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.54 % Allowed : 10.19 % Favored : 89.27 % 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: -3.44 (0.15), residues: 2140 helix: -2.52 (0.13), residues: 1056 sheet: 0.13 (0.27), residues: 352 loop : -2.91 (0.18), residues: 732 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 400 time to evaluate : 1.900 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 401 average time/residue: 0.3525 time to fit residues: 201.2878 Evaluate side-chains 361 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 357 time to evaluate : 1.929 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1674 time to fit residues: 3.8811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 160 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 208 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17148 Z= 0.224 Angle : 0.458 4.312 23156 Z= 0.247 Chirality : 0.046 0.135 2692 Planarity : 0.003 0.028 3000 Dihedral : 7.271 65.779 2480 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.27 % Allowed : 14.11 % Favored : 85.62 % 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: -2.19 (0.17), residues: 2140 helix: -1.29 (0.15), residues: 1020 sheet: 0.33 (0.27), residues: 352 loop : -2.39 (0.19), residues: 768 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 385 time to evaluate : 1.888 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 387 average time/residue: 0.3143 time to fit residues: 176.9781 Evaluate side-chains 371 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 367 time to evaluate : 2.049 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1843 time to fit residues: 4.0725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 193 optimal weight: 0.5980 chunk 204 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17148 Z= 0.136 Angle : 0.411 4.175 23156 Z= 0.222 Chirality : 0.045 0.131 2692 Planarity : 0.003 0.025 3000 Dihedral : 6.777 59.890 2480 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.49 % Allowed : 15.80 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.17), residues: 2140 helix: -0.64 (0.16), residues: 1020 sheet: 0.58 (0.27), residues: 352 loop : -2.38 (0.19), residues: 768 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 379 time to evaluate : 2.080 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 383 average time/residue: 0.3146 time to fit residues: 175.9966 Evaluate side-chains 366 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 362 time to evaluate : 1.955 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2125 time to fit residues: 4.0658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 0.0670 chunk 183 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 17148 Z= 0.136 Angle : 0.402 4.192 23156 Z= 0.216 Chirality : 0.045 0.136 2692 Planarity : 0.003 0.050 3000 Dihedral : 6.419 59.997 2480 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.44 % Allowed : 16.34 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2140 helix: -0.11 (0.16), residues: 1024 sheet: 0.72 (0.27), residues: 352 loop : -2.27 (0.19), residues: 764 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 374 time to evaluate : 2.012 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 380 average time/residue: 0.3175 time to fit residues: 175.5437 Evaluate side-chains 365 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 357 time to evaluate : 1.899 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1598 time to fit residues: 4.9599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 205 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN E 219 GLN G 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17148 Z= 0.259 Angle : 0.451 4.205 23156 Z= 0.240 Chirality : 0.047 0.131 2692 Planarity : 0.004 0.073 3000 Dihedral : 6.356 58.969 2480 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.49 % Allowed : 17.27 % Favored : 82.24 % 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: -0.91 (0.17), residues: 2140 helix: 0.03 (0.16), residues: 1020 sheet: 0.74 (0.27), residues: 352 loop : -2.08 (0.20), residues: 768 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 360 time to evaluate : 2.019 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 367 average time/residue: 0.3265 time to fit residues: 174.6723 Evaluate side-chains 352 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 349 time to evaluate : 1.770 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1456 time to fit residues: 3.2945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 204 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17148 Z= 0.217 Angle : 0.433 3.975 23156 Z= 0.231 Chirality : 0.046 0.133 2692 Planarity : 0.003 0.045 3000 Dihedral : 6.121 56.665 2480 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.60 % Allowed : 16.56 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2140 helix: 0.25 (0.16), residues: 1028 sheet: 0.83 (0.27), residues: 352 loop : -2.18 (0.20), residues: 760 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 368 time to evaluate : 1.972 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 376 average time/residue: 0.3185 time to fit residues: 171.9369 Evaluate side-chains 359 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 353 time to evaluate : 1.833 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1459 time to fit residues: 4.1137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 129 optimal weight: 0.3980 chunk 139 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17148 Z= 0.154 Angle : 0.416 4.074 23156 Z= 0.222 Chirality : 0.045 0.138 2692 Planarity : 0.003 0.038 3000 Dihedral : 5.855 55.047 2480 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.16 % Allowed : 16.83 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2140 helix: 0.52 (0.16), residues: 1024 sheet: 0.98 (0.27), residues: 352 loop : -2.15 (0.20), residues: 764 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 365 time to evaluate : 2.028 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 367 average time/residue: 0.3198 time to fit residues: 170.7380 Evaluate side-chains 357 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 355 time to evaluate : 1.941 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1832 time to fit residues: 3.5093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17148 Z= 0.251 Angle : 0.448 4.031 23156 Z= 0.239 Chirality : 0.047 0.145 2692 Planarity : 0.003 0.049 3000 Dihedral : 5.973 53.997 2480 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.05 % Allowed : 17.37 % Favored : 82.57 % 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: -0.46 (0.18), residues: 2140 helix: 0.51 (0.16), residues: 1032 sheet: 1.06 (0.27), residues: 344 loop : -2.11 (0.20), residues: 764 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 363 time to evaluate : 2.097 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 364 average time/residue: 0.3257 time to fit residues: 171.1004 Evaluate side-chains 355 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 354 time to evaluate : 1.953 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1546 time to fit residues: 3.0239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 95 optimal weight: 0.0050 chunk 139 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 129 optimal weight: 0.0470 chunk 103 optimal weight: 0.1980 chunk 133 optimal weight: 0.8980 overall best weight: 0.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17148 Z= 0.114 Angle : 0.405 7.421 23156 Z= 0.218 Chirality : 0.045 0.139 2692 Planarity : 0.003 0.041 3000 Dihedral : 5.583 52.787 2480 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 17.76 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.18), residues: 2140 helix: 0.89 (0.17), residues: 1028 sheet: 1.29 (0.27), residues: 344 loop : -2.01 (0.20), residues: 768 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.972 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.3348 time to fit residues: 175.7846 Evaluate side-chains 356 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 1.942 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 155 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.155609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.111368 restraints weight = 11874.601| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.50 r_work: 0.2966 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17148 Z= 0.151 Angle : 0.411 6.246 23156 Z= 0.220 Chirality : 0.045 0.143 2692 Planarity : 0.003 0.052 3000 Dihedral : 5.563 52.399 2480 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.05 % Allowed : 17.70 % Favored : 82.24 % 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: 0.05 (0.18), residues: 2140 helix: 0.98 (0.17), residues: 1028 sheet: 1.37 (0.26), residues: 344 loop : -1.96 (0.20), residues: 768 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4459.82 seconds wall clock time: 80 minutes 27.68 seconds (4827.68 seconds total)