Starting phenix.real_space_refine on Sun Mar 17 06:39:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bki_9405/03_2024/5bki_9405_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bki_9405/03_2024/5bki_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_9405/03_2024/5bki_9405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bki_9405/03_2024/5bki_9405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bki_9405/03_2024/5bki_9405_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bki_9405/03_2024/5bki_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-dev-5265/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: 16 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: 16 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: 16 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: 16 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: 10.28, per 1000 atoms: 0.61 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: 6.10 Conformation dependent library (CDL) restraints added in 3.3 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: 3.60 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: 5.20 Time building geometry restraints manager: 6.66 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: 596 46.59 - 69.89: 100 69.89 - 93.18: 8 93.18 - 116.48: 16 Dihedral angle restraints: 10460 sinusoidal: 4308 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 10457 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: 2.020 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: 3.780 Check model and map are aligned: 0.280 Set scattering table: 0.140 Process input model: 49.140 Find NCS groups from input model: 1.190 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.520 ------------------------------------------------------------------------------- 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 : 15.839 116.480 6508 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 123 HIS 0.005 0.002 HIS E 117 PHE 0.009 0.002 PHE G 97 TYR 0.015 0.002 TYR F 214 ARG 0.004 0.000 ARG C 116 *********************** 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 : 2.054 Fit side-chains REVERT: A 25 LEU cc_start: 0.8263 (mt) cc_final: 0.8000 (tp) REVERT: A 74 TYR cc_start: 0.8203 (m-80) cc_final: 0.7477 (m-80) REVERT: A 96 GLU cc_start: 0.8217 (tt0) cc_final: 0.7949 (tt0) REVERT: A 210 GLU cc_start: 0.7816 (tt0) cc_final: 0.7555 (tt0) REVERT: A 263 ARG cc_start: 0.8246 (ttp80) cc_final: 0.8046 (ttp80) REVERT: C 25 LEU cc_start: 0.8271 (mt) cc_final: 0.8010 (tp) REVERT: C 74 TYR cc_start: 0.8235 (m-80) cc_final: 0.7513 (m-80) REVERT: C 210 GLU cc_start: 0.7811 (tt0) cc_final: 0.7545 (tt0) REVERT: C 263 ARG cc_start: 0.8225 (ttp80) cc_final: 0.8025 (ttp80) REVERT: C 310 TYR cc_start: 0.8492 (t80) cc_final: 0.8258 (t80) REVERT: E 25 LEU cc_start: 0.8253 (mt) cc_final: 0.7975 (tp) REVERT: E 74 TYR cc_start: 0.8189 (m-80) cc_final: 0.7487 (m-80) REVERT: E 210 GLU cc_start: 0.7737 (tt0) cc_final: 0.7481 (tt0) REVERT: E 294 ILE cc_start: 0.8423 (mm) cc_final: 0.8220 (mm) REVERT: G 25 LEU cc_start: 0.8257 (mt) cc_final: 0.7987 (tp) REVERT: G 74 TYR cc_start: 0.8207 (m-80) cc_final: 0.7484 (m-80) REVERT: G 96 GLU cc_start: 0.8200 (tt0) cc_final: 0.7936 (tt0) REVERT: G 210 GLU cc_start: 0.7810 (tt0) cc_final: 0.7519 (tt0) REVERT: G 263 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7945 (ttp80) REVERT: G 294 ILE cc_start: 0.8422 (mm) cc_final: 0.8218 (mm) REVERT: B 190 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 250 MET cc_start: 0.8790 (mtt) cc_final: 0.8569 (mtt) REVERT: D 190 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7821 (mt-10) REVERT: D 250 MET cc_start: 0.8788 (mtt) cc_final: 0.8583 (mtt) REVERT: F 190 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7801 (mt-10) REVERT: F 200 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8288 (mtmt) REVERT: F 250 MET cc_start: 0.8835 (mtt) cc_final: 0.8617 (mtt) REVERT: F 263 ARG cc_start: 0.7626 (ptt90) cc_final: 0.7224 (ptm-80) REVERT: H 190 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7871 (mt-10) REVERT: H 250 MET cc_start: 0.8810 (mtt) cc_final: 0.8592 (mtt) outliers start: 8 outliers final: 4 residues processed: 437 average time/residue: 0.3495 time to fit residues: 215.5508 Evaluate side-chains 378 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 374 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain G residue 77 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 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: 0.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17148 Z= 0.159 Angle : 0.480 4.708 23156 Z= 0.263 Chirality : 0.046 0.136 2692 Planarity : 0.004 0.029 3000 Dihedral : 10.881 99.207 2508 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.33 % Allowed : 9.53 % Favored : 90.14 % 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: -3.40 (0.15), residues: 2140 helix: -2.45 (0.13), residues: 1044 sheet: 0.15 (0.27), residues: 352 loop : -2.95 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 123 HIS 0.001 0.000 HIS D 117 PHE 0.006 0.001 PHE G 75 TYR 0.013 0.001 TYR B 310 ARG 0.005 0.000 ARG F 241 *********************** 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 413 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 407 time to evaluate : 2.075 Fit side-chains REVERT: A 25 LEU cc_start: 0.7917 (mt) cc_final: 0.7618 (tp) REVERT: A 210 GLU cc_start: 0.7920 (tt0) cc_final: 0.7716 (tt0) REVERT: A 219 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8428 (mm-40) REVERT: A 263 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7800 (ttp80) REVERT: C 25 LEU cc_start: 0.7921 (mt) cc_final: 0.7635 (tp) REVERT: C 210 GLU cc_start: 0.7913 (tt0) cc_final: 0.7709 (tt0) REVERT: C 219 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8394 (mm-40) REVERT: C 263 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7784 (ttp80) REVERT: E 25 LEU cc_start: 0.7904 (mt) cc_final: 0.7606 (tp) REVERT: E 74 TYR cc_start: 0.8154 (m-80) cc_final: 0.7485 (m-80) REVERT: E 210 GLU cc_start: 0.7801 (tt0) cc_final: 0.7532 (tt0) REVERT: G 25 LEU cc_start: 0.7903 (mt) cc_final: 0.7610 (tp) REVERT: G 74 TYR cc_start: 0.8153 (m-80) cc_final: 0.7470 (m-80) REVERT: G 210 GLU cc_start: 0.7918 (tt0) cc_final: 0.7685 (tt0) REVERT: G 219 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8396 (mm-40) REVERT: G 263 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7760 (ttp80) REVERT: B 200 LYS cc_start: 0.8485 (mmtt) cc_final: 0.7786 (mtmt) REVERT: B 250 MET cc_start: 0.8325 (mtt) cc_final: 0.8047 (mtt) REVERT: D 200 LYS cc_start: 0.8436 (mmtt) cc_final: 0.7877 (mtmt) REVERT: D 250 MET cc_start: 0.8304 (mtt) cc_final: 0.8033 (mtt) REVERT: D 333 TYR cc_start: 0.8725 (t80) cc_final: 0.8413 (t80) REVERT: F 200 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8008 (mtmt) REVERT: F 250 MET cc_start: 0.8374 (mtt) cc_final: 0.8097 (mtt) REVERT: F 263 ARG cc_start: 0.7497 (ptt90) cc_final: 0.7097 (ptm-80) REVERT: F 264 MET cc_start: 0.8695 (mtm) cc_final: 0.8468 (mtp) REVERT: H 200 LYS cc_start: 0.8439 (mmtt) cc_final: 0.7954 (mtmt) REVERT: H 250 MET cc_start: 0.8313 (mtt) cc_final: 0.8033 (mtt) outliers start: 6 outliers final: 3 residues processed: 407 average time/residue: 0.3425 time to fit residues: 196.4870 Evaluate side-chains 377 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 374 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 133 GLU 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: 7.9990 chunk 160 optimal weight: 0.3980 chunk 131 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17148 Z= 0.187 Angle : 0.439 4.351 23156 Z= 0.237 Chirality : 0.046 0.132 2692 Planarity : 0.003 0.027 3000 Dihedral : 8.688 81.978 2504 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.49 % Allowed : 13.07 % Favored : 86.44 % 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: -2.09 (0.17), residues: 2140 helix: -1.17 (0.16), residues: 1016 sheet: 0.43 (0.27), residues: 352 loop : -2.44 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 123 HIS 0.002 0.001 HIS E 117 PHE 0.005 0.001 PHE B 159 TYR 0.011 0.001 TYR G 51 ARG 0.007 0.000 ARG D 241 *********************** 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 412 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 403 time to evaluate : 2.040 Fit side-chains REVERT: A 74 TYR cc_start: 0.8375 (m-80) cc_final: 0.7272 (m-80) REVERT: A 96 GLU cc_start: 0.7749 (tt0) cc_final: 0.7400 (tt0) REVERT: A 210 GLU cc_start: 0.7900 (tt0) cc_final: 0.7638 (tt0) REVERT: A 263 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7816 (ttp80) REVERT: A 313 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.7361 (mmm-85) REVERT: C 25 LEU cc_start: 0.7897 (mt) cc_final: 0.7636 (tp) REVERT: C 210 GLU cc_start: 0.7893 (tt0) cc_final: 0.7631 (tt0) REVERT: C 263 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7765 (ttp80) REVERT: C 313 ARG cc_start: 0.7573 (mmm-85) cc_final: 0.7360 (mmm-85) REVERT: E 210 GLU cc_start: 0.7887 (tt0) cc_final: 0.7602 (tt0) REVERT: G 210 GLU cc_start: 0.7893 (tt0) cc_final: 0.7624 (tt0) REVERT: G 263 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7756 (ttp80) REVERT: B 201 ILE cc_start: 0.8637 (mt) cc_final: 0.8425 (mt) REVERT: B 250 MET cc_start: 0.8389 (mtt) cc_final: 0.8169 (mtt) REVERT: D 200 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7812 (mtmt) REVERT: D 250 MET cc_start: 0.8372 (mtt) cc_final: 0.8154 (mtt) REVERT: F 250 MET cc_start: 0.8393 (mtt) cc_final: 0.8177 (mtt) REVERT: H 250 MET cc_start: 0.8383 (mtt) cc_final: 0.8171 (mtt) outliers start: 9 outliers final: 9 residues processed: 405 average time/residue: 0.3168 time to fit residues: 185.4436 Evaluate side-chains 386 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 377 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 5.9990 chunk 145 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 193 optimal weight: 0.3980 chunk 204 optimal weight: 0.1980 chunk 101 optimal weight: 0.0010 chunk 183 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 17148 Z= 0.099 Angle : 0.393 4.177 23156 Z= 0.213 Chirality : 0.044 0.134 2692 Planarity : 0.003 0.032 3000 Dihedral : 7.629 66.607 2504 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.93 % Allowed : 13.94 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2140 helix: -0.34 (0.16), residues: 996 sheet: 0.71 (0.27), residues: 352 loop : -2.34 (0.18), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 123 HIS 0.001 0.000 HIS C 117 PHE 0.022 0.001 PHE C 97 TYR 0.009 0.001 TYR C 51 ARG 0.007 0.000 ARG F 241 *********************** 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 416 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 399 time to evaluate : 2.630 Fit side-chains REVERT: A 74 TYR cc_start: 0.8323 (m-80) cc_final: 0.7232 (m-80) REVERT: A 263 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7784 (ttp80) REVERT: A 313 ARG cc_start: 0.7553 (mmm-85) cc_final: 0.7328 (mmm-85) REVERT: C 263 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7767 (ttp80) REVERT: E 74 TYR cc_start: 0.8308 (m-80) cc_final: 0.7231 (m-80) REVERT: E 313 ARG cc_start: 0.7144 (mtt180) cc_final: 0.6937 (mtt180) REVERT: G 74 TYR cc_start: 0.8292 (m-80) cc_final: 0.7231 (m-80) REVERT: G 263 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7776 (ttp80) REVERT: G 313 ARG cc_start: 0.7223 (mtt180) cc_final: 0.7013 (mtt180) REVERT: D 200 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7630 (mtmt) outliers start: 17 outliers final: 10 residues processed: 406 average time/residue: 0.3188 time to fit residues: 188.4397 Evaluate side-chains 379 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 369 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 141 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2261 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= 0.230 Angle : 0.436 4.135 23156 Z= 0.233 Chirality : 0.046 0.136 2692 Planarity : 0.003 0.053 3000 Dihedral : 7.408 58.460 2504 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.82 % Allowed : 15.96 % 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: -1.09 (0.17), residues: 2140 helix: -0.15 (0.16), residues: 1020 sheet: 0.82 (0.27), residues: 352 loop : -2.22 (0.19), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 46 HIS 0.002 0.001 HIS C 117 PHE 0.022 0.001 PHE A 97 TYR 0.013 0.001 TYR A 51 ARG 0.004 0.000 ARG F 241 *********************** 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 380 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 365 time to evaluate : 2.040 Fit side-chains REVERT: A 74 TYR cc_start: 0.8382 (m-80) cc_final: 0.7305 (m-80) REVERT: A 263 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7841 (ttp80) REVERT: A 313 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7393 (mmm-85) REVERT: C 25 LEU cc_start: 0.7893 (mt) cc_final: 0.7635 (tp) REVERT: C 263 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7781 (ttp80) REVERT: E 313 ARG cc_start: 0.7352 (mtt180) cc_final: 0.7147 (mtt180) REVERT: G 74 TYR cc_start: 0.8347 (m-80) cc_final: 0.7310 (m-80) REVERT: G 263 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7818 (ttp80) REVERT: D 200 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7747 (mtmt) REVERT: F 133 GLU cc_start: 0.7684 (pm20) cc_final: 0.7399 (pm20) outliers start: 15 outliers final: 15 residues processed: 376 average time/residue: 0.3244 time to fit residues: 174.4703 Evaluate side-chains 364 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 349 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain H residue 133 GLU 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: 1.9990 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17148 Z= 0.293 Angle : 0.462 3.975 23156 Z= 0.246 Chirality : 0.047 0.133 2692 Planarity : 0.003 0.049 3000 Dihedral : 7.364 59.182 2504 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.03 % Allowed : 16.61 % Favored : 82.35 % 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: -0.98 (0.17), residues: 2140 helix: -0.05 (0.16), residues: 1028 sheet: 0.80 (0.27), residues: 352 loop : -2.16 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 123 HIS 0.003 0.001 HIS C 117 PHE 0.018 0.001 PHE A 97 TYR 0.014 0.001 TYR E 51 ARG 0.006 0.000 ARG B 237 *********************** 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 382 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 363 time to evaluate : 1.935 Fit side-chains REVERT: A 25 LEU cc_start: 0.7876 (mt) cc_final: 0.7601 (tp) REVERT: A 74 TYR cc_start: 0.8390 (m-80) cc_final: 0.7388 (m-80) REVERT: A 263 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7820 (ttp80) REVERT: C 25 LEU cc_start: 0.7896 (mt) cc_final: 0.7636 (tp) REVERT: C 263 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7812 (ttp80) REVERT: E 25 LEU cc_start: 0.7907 (mt) cc_final: 0.7639 (tp) REVERT: E 74 TYR cc_start: 0.8369 (m-80) cc_final: 0.7355 (m-80) REVERT: G 25 LEU cc_start: 0.7876 (mt) cc_final: 0.7606 (tp) REVERT: G 74 TYR cc_start: 0.8374 (m-80) cc_final: 0.7403 (m-80) REVERT: G 263 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7813 (ttp80) REVERT: D 200 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7819 (mtmt) REVERT: F 133 GLU cc_start: 0.7848 (pm20) cc_final: 0.7551 (pm20) outliers start: 19 outliers final: 17 residues processed: 378 average time/residue: 0.3287 time to fit residues: 177.9503 Evaluate side-chains 369 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 352 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 204 optimal weight: 0.1980 chunk 127 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2471 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= 0.141 Angle : 0.406 4.009 23156 Z= 0.218 Chirality : 0.045 0.133 2692 Planarity : 0.003 0.064 3000 Dihedral : 6.928 59.702 2504 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.98 % Allowed : 16.94 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2140 helix: 0.39 (0.16), residues: 1024 sheet: 1.07 (0.27), residues: 344 loop : -2.12 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 123 HIS 0.001 0.000 HIS B 117 PHE 0.016 0.001 PHE A 97 TYR 0.011 0.001 TYR A 51 ARG 0.007 0.000 ARG H 241 *********************** 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 375 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 357 time to evaluate : 2.042 Fit side-chains REVERT: A 74 TYR cc_start: 0.8394 (m-80) cc_final: 0.7354 (m-80) REVERT: A 263 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7796 (ttp80) REVERT: C 25 LEU cc_start: 0.7908 (mt) cc_final: 0.7639 (tp) REVERT: E 74 TYR cc_start: 0.8339 (m-80) cc_final: 0.7284 (m-80) REVERT: G 74 TYR cc_start: 0.8419 (m-80) cc_final: 0.7433 (m-80) REVERT: D 200 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7618 (mtmt) REVERT: F 133 GLU cc_start: 0.7689 (pm20) cc_final: 0.7438 (pm20) outliers start: 18 outliers final: 14 residues processed: 369 average time/residue: 0.3090 time to fit residues: 163.9766 Evaluate side-chains 364 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 350 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.3980 chunk 122 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 129 optimal weight: 0.1980 chunk 139 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2447 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= 0.247 Angle : 0.445 4.038 23156 Z= 0.237 Chirality : 0.047 0.137 2692 Planarity : 0.004 0.057 3000 Dihedral : 6.937 59.205 2504 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.87 % Allowed : 16.94 % Favored : 82.19 % 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: -0.54 (0.18), residues: 2140 helix: 0.41 (0.16), residues: 1024 sheet: 1.08 (0.27), residues: 344 loop : -2.10 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 123 HIS 0.002 0.001 HIS E 117 PHE 0.016 0.001 PHE A 97 TYR 0.012 0.001 TYR E 51 ARG 0.008 0.000 ARG G 263 *********************** 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 372 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 356 time to evaluate : 2.144 Fit side-chains REVERT: A 25 LEU cc_start: 0.7899 (mt) cc_final: 0.7637 (tp) REVERT: A 74 TYR cc_start: 0.8409 (m-80) cc_final: 0.7363 (m-80) REVERT: A 263 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7770 (ttp80) REVERT: A 264 MET cc_start: 0.8752 (ttm) cc_final: 0.8244 (ttm) REVERT: C 25 LEU cc_start: 0.7884 (mt) cc_final: 0.7624 (tp) REVERT: E 25 LEU cc_start: 0.7896 (mt) cc_final: 0.7632 (tp) REVERT: G 25 LEU cc_start: 0.7898 (mt) cc_final: 0.7639 (tp) REVERT: G 74 TYR cc_start: 0.8438 (m-80) cc_final: 0.7438 (m-80) REVERT: D 200 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7762 (mtmt) outliers start: 16 outliers final: 16 residues processed: 367 average time/residue: 0.3082 time to fit residues: 163.9187 Evaluate side-chains 367 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 351 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17148 Z= 0.185 Angle : 0.420 3.934 23156 Z= 0.225 Chirality : 0.046 0.142 2692 Planarity : 0.003 0.042 3000 Dihedral : 6.707 58.045 2504 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.82 % Allowed : 17.21 % Favored : 81.97 % 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: -0.33 (0.18), residues: 2140 helix: 0.60 (0.16), residues: 1028 sheet: 1.19 (0.27), residues: 344 loop : -2.05 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 123 HIS 0.002 0.000 HIS B 117 PHE 0.015 0.001 PHE A 97 TYR 0.011 0.001 TYR C 51 ARG 0.009 0.000 ARG C 263 *********************** 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 367 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 352 time to evaluate : 2.152 Fit side-chains REVERT: A 25 LEU cc_start: 0.7904 (mt) cc_final: 0.7635 (tp) REVERT: A 74 TYR cc_start: 0.8406 (m-80) cc_final: 0.7367 (m-80) REVERT: A 263 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7742 (ttp80) REVERT: A 264 MET cc_start: 0.8734 (ttm) cc_final: 0.8215 (ttm) REVERT: C 25 LEU cc_start: 0.7876 (mt) cc_final: 0.7612 (tp) REVERT: E 25 LEU cc_start: 0.7897 (mt) cc_final: 0.7628 (tp) REVERT: E 74 TYR cc_start: 0.8423 (m-80) cc_final: 0.7390 (m-80) REVERT: G 74 TYR cc_start: 0.8437 (m-80) cc_final: 0.7441 (m-80) REVERT: D 200 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7579 (mtmt) outliers start: 15 outliers final: 14 residues processed: 361 average time/residue: 0.3192 time to fit residues: 165.7273 Evaluate side-chains 359 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 345 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 139 optimal weight: 0.6980 chunk 211 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 129 optimal weight: 0.1980 chunk 103 optimal weight: 0.0020 chunk 133 optimal weight: 0.7980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 17148 Z= 0.108 Angle : 0.392 4.274 23156 Z= 0.211 Chirality : 0.044 0.139 2692 Planarity : 0.003 0.034 3000 Dihedral : 6.315 58.116 2504 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.93 % Allowed : 17.10 % Favored : 81.97 % 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: 0.08 (0.18), residues: 2140 helix: 1.02 (0.17), residues: 1012 sheet: 1.48 (0.27), residues: 344 loop : -1.97 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 123 HIS 0.001 0.000 HIS D 117 PHE 0.014 0.001 PHE A 97 TYR 0.009 0.001 TYR A 51 ARG 0.008 0.000 ARG C 263 ********************** 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 372 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 355 time to evaluate : 1.867 Fit side-chains REVERT: A 25 LEU cc_start: 0.7889 (mt) cc_final: 0.7624 (tp) REVERT: A 74 TYR cc_start: 0.8442 (m-80) cc_final: 0.7346 (m-80) REVERT: A 263 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7732 (ttp80) REVERT: A 264 MET cc_start: 0.8710 (ttm) cc_final: 0.8206 (ttm) REVERT: E 25 LEU cc_start: 0.7842 (mt) cc_final: 0.7580 (tp) REVERT: G 25 LEU cc_start: 0.7890 (mt) cc_final: 0.7628 (tp) REVERT: G 74 TYR cc_start: 0.8413 (m-80) cc_final: 0.7363 (m-80) REVERT: D 200 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7466 (mtmt) outliers start: 17 outliers final: 14 residues processed: 365 average time/residue: 0.3154 time to fit residues: 165.9338 Evaluate side-chains 361 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 347 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain H residue 133 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 70 optimal weight: 0.1980 chunk 172 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.154856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.110502 restraints weight = 11736.277| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.50 r_work: 0.2958 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17148 Z= 0.173 Angle : 0.413 3.992 23156 Z= 0.221 Chirality : 0.045 0.146 2692 Planarity : 0.003 0.038 3000 Dihedral : 6.334 56.541 2504 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.87 % Allowed : 17.48 % Favored : 81.64 % 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: 0.10 (0.18), residues: 2140 helix: 0.98 (0.17), residues: 1028 sheet: 1.52 (0.26), residues: 344 loop : -1.96 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 123 HIS 0.001 0.000 HIS D 117 PHE 0.008 0.001 PHE E 97 TYR 0.010 0.001 TYR E 51 ARG 0.007 0.000 ARG C 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4498.41 seconds wall clock time: 80 minutes 52.09 seconds (4852.09 seconds total)