Starting phenix.real_space_refine on Sun Apr 7 07:01:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpe_0743/04_2024/6kpe_0743.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpe_0743/04_2024/6kpe_0743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpe_0743/04_2024/6kpe_0743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpe_0743/04_2024/6kpe_0743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpe_0743/04_2024/6kpe_0743.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpe_0743/04_2024/6kpe_0743.pdb" } resolution = 2.83 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= -0.007 sd= 0.312 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 Mg 12 5.21 5 S 120 5.16 5 C 20004 2.51 5 N 5076 2.21 5 O 5760 1.98 5 H 31212 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 2": "OD1" <-> "OD2" Residue "A ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "B ASP 2": "OD1" <-> "OD2" Residue "B ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "C ASP 2": "OD1" <-> "OD2" Residue "C ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "D ASP 2": "OD1" <-> "OD2" Residue "D ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 314": "OE1" <-> "OE2" Residue "E ASP 2": "OD1" <-> "OD2" Residue "E ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 314": "OE1" <-> "OE2" Residue "F ASP 2": "OD1" <-> "OD2" Residue "F ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 314": "OE1" <-> "OE2" Residue "G ASP 2": "OD1" <-> "OD2" Residue "G ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 314": "OE1" <-> "OE2" Residue "H ASP 2": "OD1" <-> "OD2" Residue "H ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 314": "OE1" <-> "OE2" Residue "I ASP 2": "OD1" <-> "OD2" Residue "I ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 314": "OE1" <-> "OE2" Residue "J ASP 2": "OD1" <-> "OD2" Residue "J ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 314": "OE1" <-> "OE2" Residue "K ASP 2": "OD1" <-> "OD2" Residue "K ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 314": "OE1" <-> "OE2" Residue "L ASP 2": "OD1" <-> "OD2" Residue "L ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 314": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 62184 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "B" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "C" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "D" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "E" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "F" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "G" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "H" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "I" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "J" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "K" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "L" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.03, per 1000 atoms: 0.32 Number of scatterers: 62184 At special positions: 0 Unit cell: (143.64, 143.64, 143.64, 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) S 120 16.00 Mg 12 11.99 O 5760 8.00 N 5076 7.00 C 20004 6.00 H 31212 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.47 Conformation dependent library (CDL) restraints added in 4.9 seconds 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 12 sheets defined 64.9% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 85 through 91 Processing helix chain 'A' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.749A pdb=" N MET A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 removed outlier: 3.605A pdb=" N ALA A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 Processing helix chain 'A' and resid 247 through 253 Processing helix chain 'A' and resid 254 through 286 removed outlier: 5.826A pdb=" N ASP A 270 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 286 " --> pdb=" O TYR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'B' and resid 26 through 37 Processing helix chain 'B' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU B 52 " --> pdb=" O ASP B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 85 through 91 Processing helix chain 'B' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 139 " --> pdb=" O GLY B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 171 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.606A pdb=" N ALA B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP B 270 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B 271 " --> pdb=" O LYS B 267 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 286 " --> pdb=" O TYR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 Processing helix chain 'B' and resid 300 through 312 Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 48 through 56 removed outlier: 3.656A pdb=" N GLU C 52 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 85 through 91 Processing helix chain 'C' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET C 137 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 139 " --> pdb=" O GLY C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 171 Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 217 removed outlier: 3.583A pdb=" N ILE C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 229 removed outlier: 3.606A pdb=" N ALA C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 244 Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP C 270 " --> pdb=" O PHE C 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 271 " --> pdb=" O LYS C 267 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 286 " --> pdb=" O TYR C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 313 through 326 Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'D' and resid 85 through 91 Processing helix chain 'D' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 113 Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET D 137 " --> pdb=" O GLY D 133 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 139 " --> pdb=" O GLY D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 229 removed outlier: 3.605A pdb=" N ALA D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 244 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP D 270 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL D 271 " --> pdb=" O LYS D 267 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY D 286 " --> pdb=" O TYR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 313 through 326 Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 48 through 56 removed outlier: 3.656A pdb=" N GLU E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 71 Processing helix chain 'E' and resid 85 through 91 Processing helix chain 'E' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 Processing helix chain 'E' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU E 139 " --> pdb=" O GLY E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU E 187 " --> pdb=" O SER E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 217 removed outlier: 3.583A pdb=" N ILE E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 229 removed outlier: 3.605A pdb=" N ALA E 224 " --> pdb=" O SER E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 244 Processing helix chain 'E' and resid 247 through 253 Processing helix chain 'E' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP E 270 " --> pdb=" O PHE E 266 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL E 271 " --> pdb=" O LYS E 267 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL E 272 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY E 286 " --> pdb=" O TYR E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 299 Processing helix chain 'E' and resid 300 through 312 Processing helix chain 'E' and resid 313 through 326 Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU F 52 " --> pdb=" O ASP F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 Processing helix chain 'F' and resid 85 through 91 Processing helix chain 'F' and resid 91 through 96 removed outlier: 4.291A pdb=" N GLN F 96 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 113 Processing helix chain 'F' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET F 137 " --> pdb=" O GLY F 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 139 " --> pdb=" O GLY F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 229 removed outlier: 3.605A pdb=" N ALA F 224 " --> pdb=" O SER F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 244 Processing helix chain 'F' and resid 247 through 253 Processing helix chain 'F' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP F 270 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL F 271 " --> pdb=" O LYS F 267 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY F 286 " --> pdb=" O TYR F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 299 Processing helix chain 'F' and resid 300 through 312 Processing helix chain 'F' and resid 313 through 326 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 48 through 56 removed outlier: 3.656A pdb=" N GLU G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 71 Processing helix chain 'G' and resid 85 through 91 Processing helix chain 'G' and resid 91 through 96 removed outlier: 4.291A pdb=" N GLN G 96 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 113 Processing helix chain 'G' and resid 133 through 143 removed outlier: 3.749A pdb=" N MET G 137 " --> pdb=" O GLY G 133 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU G 139 " --> pdb=" O GLY G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 171 Processing helix chain 'G' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU G 187 " --> pdb=" O SER G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 217 removed outlier: 3.583A pdb=" N ILE G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 229 removed outlier: 3.605A pdb=" N ALA G 224 " --> pdb=" O SER G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 244 Processing helix chain 'G' and resid 247 through 253 Processing helix chain 'G' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP G 270 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL G 271 " --> pdb=" O LYS G 267 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL G 272 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY G 286 " --> pdb=" O TYR G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 299 Processing helix chain 'G' and resid 300 through 312 Processing helix chain 'G' and resid 313 through 326 Processing helix chain 'H' and resid 26 through 37 Processing helix chain 'H' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU H 52 " --> pdb=" O ASP H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 71 Processing helix chain 'H' and resid 85 through 91 Processing helix chain 'H' and resid 91 through 96 removed outlier: 4.291A pdb=" N GLN H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 Processing helix chain 'H' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET H 137 " --> pdb=" O GLY H 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP H 138 " --> pdb=" O GLU H 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU H 139 " --> pdb=" O GLY H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 171 Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.616A pdb=" N GLU H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 229 removed outlier: 3.605A pdb=" N ALA H 224 " --> pdb=" O SER H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 244 Processing helix chain 'H' and resid 247 through 253 Processing helix chain 'H' and resid 254 through 286 removed outlier: 5.826A pdb=" N ASP H 270 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL H 271 " --> pdb=" O LYS H 267 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 299 Processing helix chain 'H' and resid 300 through 312 Processing helix chain 'H' and resid 313 through 326 Processing helix chain 'I' and resid 26 through 37 Processing helix chain 'I' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU I 52 " --> pdb=" O ASP I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 71 Processing helix chain 'I' and resid 85 through 91 Processing helix chain 'I' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN I 96 " --> pdb=" O ALA I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 113 Processing helix chain 'I' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET I 137 " --> pdb=" O GLY I 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP I 138 " --> pdb=" O GLU I 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU I 139 " --> pdb=" O GLY I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 Processing helix chain 'I' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU I 187 " --> pdb=" O SER I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE I 201 " --> pdb=" O THR I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 229 removed outlier: 3.606A pdb=" N ALA I 224 " --> pdb=" O SER I 220 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 244 Processing helix chain 'I' and resid 247 through 253 Processing helix chain 'I' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP I 270 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL I 271 " --> pdb=" O LYS I 267 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL I 272 " --> pdb=" O TYR I 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY I 286 " --> pdb=" O TYR I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 299 Processing helix chain 'I' and resid 300 through 312 Processing helix chain 'I' and resid 313 through 326 Processing helix chain 'J' and resid 26 through 37 Processing helix chain 'J' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU J 52 " --> pdb=" O ASP J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 71 Processing helix chain 'J' and resid 85 through 91 Processing helix chain 'J' and resid 91 through 96 removed outlier: 4.291A pdb=" N GLN J 96 " --> pdb=" O ALA J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 113 Processing helix chain 'J' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET J 137 " --> pdb=" O GLY J 133 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU J 139 " --> pdb=" O GLY J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 171 Processing helix chain 'J' and resid 183 through 197 removed outlier: 3.616A pdb=" N GLU J 187 " --> pdb=" O SER J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE J 201 " --> pdb=" O THR J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 229 removed outlier: 3.606A pdb=" N ALA J 224 " --> pdb=" O SER J 220 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 244 Processing helix chain 'J' and resid 247 through 253 Processing helix chain 'J' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP J 270 " --> pdb=" O PHE J 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL J 271 " --> pdb=" O LYS J 267 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY J 286 " --> pdb=" O TYR J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 299 Processing helix chain 'J' and resid 300 through 312 Processing helix chain 'J' and resid 313 through 326 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 71 Processing helix chain 'K' and resid 85 through 91 Processing helix chain 'K' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 113 Processing helix chain 'K' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET K 137 " --> pdb=" O GLY K 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP K 138 " --> pdb=" O GLU K 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU K 139 " --> pdb=" O GLY K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 Processing helix chain 'K' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU K 187 " --> pdb=" O SER K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE K 201 " --> pdb=" O THR K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 229 removed outlier: 3.606A pdb=" N ALA K 224 " --> pdb=" O SER K 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 244 Processing helix chain 'K' and resid 247 through 253 Processing helix chain 'K' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP K 270 " --> pdb=" O PHE K 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL K 271 " --> pdb=" O LYS K 267 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL K 272 " --> pdb=" O TYR K 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY K 286 " --> pdb=" O TYR K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 299 Processing helix chain 'K' and resid 300 through 312 Processing helix chain 'K' and resid 313 through 326 Processing helix chain 'L' and resid 26 through 37 Processing helix chain 'L' and resid 48 through 56 removed outlier: 3.655A pdb=" N GLU L 52 " --> pdb=" O ASP L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 71 Processing helix chain 'L' and resid 85 through 91 Processing helix chain 'L' and resid 91 through 96 removed outlier: 4.292A pdb=" N GLN L 96 " --> pdb=" O ALA L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 113 Processing helix chain 'L' and resid 133 through 143 removed outlier: 3.748A pdb=" N MET L 137 " --> pdb=" O GLY L 133 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP L 138 " --> pdb=" O GLU L 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU L 139 " --> pdb=" O GLY L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 Processing helix chain 'L' and resid 183 through 197 removed outlier: 3.617A pdb=" N GLU L 187 " --> pdb=" O SER L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 217 removed outlier: 3.584A pdb=" N ILE L 201 " --> pdb=" O THR L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 229 removed outlier: 3.605A pdb=" N ALA L 224 " --> pdb=" O SER L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 244 Processing helix chain 'L' and resid 247 through 253 Processing helix chain 'L' and resid 254 through 286 removed outlier: 5.827A pdb=" N ASP L 270 " --> pdb=" O PHE L 266 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL L 271 " --> pdb=" O LYS L 267 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY L 286 " --> pdb=" O TYR L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 299 Processing helix chain 'L' and resid 300 through 312 Processing helix chain 'L' and resid 313 through 326 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 7.271A pdb=" N VAL A 148 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR A 124 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA A 74 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 42 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL B 148 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR B 124 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE B 105 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 74 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 42 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 5 removed outlier: 7.271A pdb=" N VAL C 148 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR C 124 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE C 105 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 74 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 42 " --> pdb=" O ILE C 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL D 148 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR D 124 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE D 105 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA D 74 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D 42 " --> pdb=" O ILE D 18 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 4 through 5 removed outlier: 7.269A pdb=" N VAL E 148 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR E 124 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE E 105 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA E 74 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE E 42 " --> pdb=" O ILE E 18 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL F 148 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR F 124 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE F 105 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA F 74 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE F 42 " --> pdb=" O ILE F 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL G 148 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR G 124 " --> pdb=" O LYS G 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE G 105 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA G 74 " --> pdb=" O ASP G 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE G 42 " --> pdb=" O ILE G 18 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL H 148 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR H 124 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA H 74 " --> pdb=" O ASP H 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE H 42 " --> pdb=" O ILE H 18 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL I 148 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR I 124 " --> pdb=" O LYS I 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE I 105 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA I 74 " --> pdb=" O ASP I 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE I 42 " --> pdb=" O ILE I 18 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL J 148 " --> pdb=" O VAL J 180 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR J 124 " --> pdb=" O LYS J 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE J 105 " --> pdb=" O ILE J 125 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA J 74 " --> pdb=" O ASP J 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE J 42 " --> pdb=" O ILE J 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL K 148 " --> pdb=" O VAL K 180 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR K 124 " --> pdb=" O LYS K 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE K 105 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA K 74 " --> pdb=" O ASP K 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE K 42 " --> pdb=" O ILE K 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 5 removed outlier: 7.270A pdb=" N VAL L 148 " --> pdb=" O VAL L 180 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR L 124 " --> pdb=" O LYS L 153 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE L 105 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA L 74 " --> pdb=" O ASP L 104 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE L 42 " --> pdb=" O ILE L 18 " (cutoff:3.500A) 1788 hydrogen bonds defined for protein. 5184 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: 20.11 Time building geometry restraints manager: 43.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 31198 1.02 - 1.22: 14 1.22 - 1.41: 12993 1.41 - 1.61: 18375 1.61 - 1.80: 228 Bond restraints: 62808 Sorted by residual: bond pdb=" CB SER E 121 " pdb=" HB3 SER E 121 " ideal model delta sigma weight residual 0.970 1.064 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" CB SER E 121 " pdb=" HB2 SER E 121 " ideal model delta sigma weight residual 0.970 1.025 -0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" OG SER E 121 " pdb=" HG SER E 121 " ideal model delta sigma weight residual 0.840 0.885 -0.045 2.00e-02 2.50e+03 5.04e+00 bond pdb=" CB SER H 121 " pdb=" HB2 SER H 121 " ideal model delta sigma weight residual 0.970 1.006 -0.036 2.00e-02 2.50e+03 3.17e+00 bond pdb=" CB ASP K 80 " pdb=" HB2 ASP K 80 " ideal model delta sigma weight residual 0.970 1.005 -0.035 2.00e-02 2.50e+03 3.12e+00 ... (remaining 62803 not shown) Histogram of bond angle deviations from ideal: 70.08 - 83.31: 311 83.31 - 96.55: 47 96.55 - 109.78: 48252 109.78 - 123.01: 59156 123.01 - 136.25: 6186 Bond angle restraints: 113952 Sorted by residual: angle pdb=" CG2 VAL C 68 " pdb=" CB VAL C 68 " pdb=" HB VAL C 68 " ideal model delta sigma weight residual 108.00 70.08 37.92 3.00e+00 1.11e-01 1.60e+02 angle pdb=" CG2 ILE G 171 " pdb=" CB ILE G 171 " pdb=" HB ILE G 171 " ideal model delta sigma weight residual 109.00 71.41 37.59 3.00e+00 1.11e-01 1.57e+02 angle pdb=" CG1 ILE J 174 " pdb=" CB ILE J 174 " pdb=" HB ILE J 174 " ideal model delta sigma weight residual 109.00 71.94 37.06 3.00e+00 1.11e-01 1.53e+02 angle pdb=" CG1 ILE I 178 " pdb=" CB ILE I 178 " pdb=" HB ILE I 178 " ideal model delta sigma weight residual 109.00 71.97 37.03 3.00e+00 1.11e-01 1.52e+02 angle pdb=" CG1 ILE G 171 " pdb=" CB ILE G 171 " pdb=" HB ILE G 171 " ideal model delta sigma weight residual 109.00 72.20 36.80 3.00e+00 1.11e-01 1.50e+02 ... (remaining 113947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 25996 17.51 - 35.03: 2455 35.03 - 52.54: 536 52.54 - 70.05: 219 70.05 - 87.57: 14 Dihedral angle restraints: 29220 sinusoidal: 15864 harmonic: 13356 Sorted by residual: dihedral pdb=" CA LYS B 14 " pdb=" C LYS B 14 " pdb=" N GLY B 15 " pdb=" CA GLY B 15 " ideal model delta harmonic sigma weight residual -180.00 -157.17 -22.83 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA LYS L 14 " pdb=" C LYS L 14 " pdb=" N GLY L 15 " pdb=" CA GLY L 15 " ideal model delta harmonic sigma weight residual -180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LYS G 14 " pdb=" C LYS G 14 " pdb=" N GLY G 15 " pdb=" CA GLY G 15 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 29217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.322: 4632 0.322 - 0.645: 0 0.645 - 0.967: 0 0.967 - 1.289: 0 1.289 - 1.612: 36 Chirality restraints: 4668 Sorted by residual: chirality pdb=" CB VAL B 29 " pdb=" CA VAL B 29 " pdb=" CG1 VAL B 29 " pdb=" CG2 VAL B 29 " both_signs ideal model delta sigma weight residual False -2.63 -1.02 -1.61 2.00e-01 2.50e+01 6.49e+01 chirality pdb=" CB VAL C 29 " pdb=" CA VAL C 29 " pdb=" CG1 VAL C 29 " pdb=" CG2 VAL C 29 " both_signs ideal model delta sigma weight residual False -2.63 -1.02 -1.61 2.00e-01 2.50e+01 6.49e+01 chirality pdb=" CB VAL F 29 " pdb=" CA VAL F 29 " pdb=" CG1 VAL F 29 " pdb=" CG2 VAL F 29 " both_signs ideal model delta sigma weight residual False -2.63 -1.02 -1.61 2.00e-01 2.50e+01 6.49e+01 ... (remaining 4665 not shown) Planarity restraints: 9204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 128 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.39e+00 pdb=" N PRO A 129 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 128 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO E 129 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 129 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 129 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA J 128 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO J 129 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO J 129 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 129 " -0.025 5.00e-02 4.00e+02 ... (remaining 9201 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 2785 2.13 - 2.75: 121437 2.75 - 3.37: 172163 3.37 - 3.98: 223179 3.98 - 4.60: 360445 Nonbonded interactions: 880009 Sorted by model distance: nonbonded pdb=" OE1 GLU E 222 " pdb=" H GLU E 222 " model vdw 1.514 1.850 nonbonded pdb=" OE1 GLU A 222 " pdb=" H GLU A 222 " model vdw 1.514 1.850 nonbonded pdb=" OE1 GLU D 222 " pdb=" H GLU D 222 " model vdw 1.515 1.850 nonbonded pdb=" OE1 GLU B 222 " pdb=" H GLU B 222 " model vdw 1.515 1.850 nonbonded pdb=" OE1 GLU H 222 " pdb=" H GLU H 222 " model vdw 1.515 1.850 ... (remaining 880004 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.200 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: 0.690 Extract box with map and model: 11.350 Check model and map are aligned: 0.690 Set scattering table: 0.460 Process input model: 152.320 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.340 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: 0.000 Load rotamer database and sin/cos tables:10.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.009 0.042 31596 Z= 0.566 Angle : 0.818 11.350 42660 Z= 0.446 Chirality : 0.142 1.612 4668 Planarity : 0.004 0.046 5424 Dihedral : 13.073 67.361 11736 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -5.24 (0.10), residues: 3912 helix: -3.06 (0.08), residues: 2172 sheet: -4.07 (0.21), residues: 264 loop : -3.79 (0.13), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 198 HIS 0.006 0.002 HIS I 140 PHE 0.008 0.001 PHE A 303 TYR 0.011 0.002 TYR C 300 ARG 0.002 0.000 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 609 time to evaluate : 3.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8974 (tmt170) cc_final: 0.8268 (tmm-80) REVERT: B 28 ARG cc_start: 0.8989 (tmt170) cc_final: 0.8314 (tmm-80) REVERT: C 28 ARG cc_start: 0.8939 (tmt170) cc_final: 0.8243 (tmm-80) REVERT: C 75 LEU cc_start: 0.8825 (mt) cc_final: 0.8530 (mt) REVERT: C 320 LYS cc_start: 0.8825 (tttt) cc_final: 0.8575 (tptt) REVERT: D 28 ARG cc_start: 0.8971 (tmt170) cc_final: 0.8266 (tmm-80) REVERT: D 320 LYS cc_start: 0.8862 (tttt) cc_final: 0.8644 (tptt) REVERT: F 28 ARG cc_start: 0.8949 (tmt170) cc_final: 0.8297 (tmm-80) REVERT: F 216 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8220 (tm-30) REVERT: F 320 LYS cc_start: 0.8733 (tttt) cc_final: 0.8506 (tptt) REVERT: G 28 ARG cc_start: 0.8954 (tmt170) cc_final: 0.8212 (tmm-80) REVERT: G 320 LYS cc_start: 0.8908 (tttt) cc_final: 0.8702 (tptt) REVERT: H 28 ARG cc_start: 0.8951 (tmt170) cc_final: 0.8203 (tmm-80) REVERT: H 267 LYS cc_start: 0.9585 (tttp) cc_final: 0.9252 (tttm) REVERT: H 320 LYS cc_start: 0.8919 (tttt) cc_final: 0.8709 (tptt) REVERT: I 28 ARG cc_start: 0.8889 (tmt170) cc_final: 0.8134 (tmm160) REVERT: I 124 THR cc_start: 0.9335 (m) cc_final: 0.8726 (p) REVERT: I 320 LYS cc_start: 0.8943 (tttt) cc_final: 0.8737 (tptt) REVERT: J 28 ARG cc_start: 0.8960 (tmt170) cc_final: 0.8229 (tmm-80) REVERT: J 320 LYS cc_start: 0.8906 (tttt) cc_final: 0.8696 (tptt) REVERT: K 28 ARG cc_start: 0.8891 (tmt170) cc_final: 0.8150 (tmm-80) REVERT: K 124 THR cc_start: 0.9343 (m) cc_final: 0.8744 (p) REVERT: K 320 LYS cc_start: 0.8876 (tttt) cc_final: 0.8673 (tptt) REVERT: L 28 ARG cc_start: 0.8941 (tmt170) cc_final: 0.8211 (tmm-80) REVERT: L 216 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8232 (tm-30) REVERT: L 320 LYS cc_start: 0.8833 (tttt) cc_final: 0.8605 (tptt) outliers start: 0 outliers final: 0 residues processed: 609 average time/residue: 3.3311 time to fit residues: 2309.5547 Evaluate side-chains 390 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 3.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 155 optimal weight: 0.6980 chunk 300 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 348 optimal weight: 0.6980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 142 GLN A 154 GLN A 278 ASN A 296 GLN B 96 GLN B 142 GLN B 154 GLN B 278 ASN B 296 GLN C 96 GLN C 142 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN C 296 GLN D 96 GLN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 ASN D 296 GLN E 96 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN E 278 ASN E 296 GLN F 96 GLN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 GLN F 278 ASN F 296 GLN G 96 GLN G 142 GLN ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 GLN G 278 ASN G 296 GLN H 96 GLN H 142 GLN ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 278 ASN H 296 GLN I 96 GLN ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 GLN I 278 ASN I 296 GLN J 96 GLN ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 GLN J 278 ASN J 296 GLN K 96 GLN ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 GLN K 278 ASN K 296 GLN L 96 GLN ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN L 278 ASN L 296 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 31596 Z= 0.316 Angle : 0.807 16.092 42660 Z= 0.420 Chirality : 0.157 1.737 4668 Planarity : 0.004 0.041 5424 Dihedral : 5.220 21.528 4284 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.12 % Allowed : 12.23 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -2.95 (0.12), residues: 3912 helix: -1.02 (0.10), residues: 2292 sheet: -3.06 (0.17), residues: 408 loop : -3.16 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 198 HIS 0.005 0.002 HIS F 140 PHE 0.010 0.002 PHE H 288 TYR 0.010 0.001 TYR E 229 ARG 0.011 0.001 ARG I 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 422 time to evaluate : 3.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.9196 (mt) cc_final: 0.8809 (mt) REVERT: A 167 ILE cc_start: 0.9682 (mt) cc_final: 0.9462 (tp) REVERT: B 75 LEU cc_start: 0.9055 (mt) cc_final: 0.8648 (mt) REVERT: C 167 ILE cc_start: 0.9665 (mt) cc_final: 0.9407 (tp) REVERT: C 320 LYS cc_start: 0.9052 (tttt) cc_final: 0.8735 (tptt) REVERT: D 28 ARG cc_start: 0.9022 (tmt170) cc_final: 0.8341 (tmm-80) REVERT: D 30 GLN cc_start: 0.8349 (mp10) cc_final: 0.8141 (mp10) REVERT: D 167 ILE cc_start: 0.9666 (mt) cc_final: 0.9431 (tp) REVERT: D 320 LYS cc_start: 0.9078 (tttt) cc_final: 0.8780 (tptt) REVERT: E 267 LYS cc_start: 0.9626 (OUTLIER) cc_final: 0.9421 (ttpp) REVERT: F 75 LEU cc_start: 0.9068 (mt) cc_final: 0.8647 (mt) REVERT: F 167 ILE cc_start: 0.9673 (mt) cc_final: 0.9420 (tp) REVERT: F 320 LYS cc_start: 0.9006 (tttt) cc_final: 0.8695 (tptt) REVERT: G 28 ARG cc_start: 0.9014 (tmt170) cc_final: 0.8280 (tmm-80) REVERT: G 167 ILE cc_start: 0.9662 (mt) cc_final: 0.9436 (tp) REVERT: G 320 LYS cc_start: 0.9147 (tttt) cc_final: 0.8878 (tptt) REVERT: H 167 ILE cc_start: 0.9668 (mt) cc_final: 0.9415 (tp) REVERT: H 267 LYS cc_start: 0.9603 (tttp) cc_final: 0.9287 (tttm) REVERT: H 320 LYS cc_start: 0.9136 (tttt) cc_final: 0.8856 (tptt) REVERT: I 167 ILE cc_start: 0.9679 (mt) cc_final: 0.9449 (tp) REVERT: I 320 LYS cc_start: 0.9134 (tttt) cc_final: 0.8850 (tptt) REVERT: J 167 ILE cc_start: 0.9665 (mt) cc_final: 0.9407 (tp) REVERT: J 320 LYS cc_start: 0.9131 (tttt) cc_final: 0.8831 (tptt) REVERT: K 28 ARG cc_start: 0.8963 (tmt170) cc_final: 0.8197 (tmm-80) REVERT: K 320 LYS cc_start: 0.9081 (tttt) cc_final: 0.8808 (tptt) REVERT: L 80 ASP cc_start: 0.8818 (m-30) cc_final: 0.8478 (p0) REVERT: L 167 ILE cc_start: 0.9668 (mt) cc_final: 0.9432 (tp) REVERT: L 320 LYS cc_start: 0.9074 (tttt) cc_final: 0.8775 (tptt) outliers start: 68 outliers final: 26 residues processed: 466 average time/residue: 2.9541 time to fit residues: 1597.3413 Evaluate side-chains 395 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 368 time to evaluate : 3.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 267 LYS Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 99 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 290 optimal weight: 6.9990 chunk 237 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 1.9990 chunk 377 optimal weight: 3.9990 chunk 311 optimal weight: 7.9990 chunk 346 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 280 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 GLN D 110 ASN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN E 110 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN G 154 GLN H 154 GLN I 110 ASN ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 GLN J 110 ASN ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 GLN ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 ASN ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31596 Z= 0.279 Angle : 0.748 15.857 42660 Z= 0.382 Chirality : 0.158 1.841 4668 Planarity : 0.004 0.045 5424 Dihedral : 4.961 20.006 4284 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.47 % Allowed : 13.67 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.90 (0.13), residues: 3912 helix: -0.23 (0.10), residues: 2304 sheet: -2.38 (0.19), residues: 408 loop : -2.73 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 198 HIS 0.005 0.002 HIS L 196 PHE 0.010 0.001 PHE G 288 TYR 0.010 0.001 TYR L 217 ARG 0.006 0.001 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 379 time to evaluate : 3.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 320 LYS cc_start: 0.9079 (tttt) cc_final: 0.8753 (tptt) REVERT: D 320 LYS cc_start: 0.9124 (tttt) cc_final: 0.8864 (tptt) REVERT: E 178 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8902 (pp) REVERT: E 267 LYS cc_start: 0.9597 (OUTLIER) cc_final: 0.9395 (ttpp) REVERT: F 320 LYS cc_start: 0.9055 (tttt) cc_final: 0.8738 (tptt) REVERT: G 320 LYS cc_start: 0.9170 (tttt) cc_final: 0.8897 (tptt) REVERT: H 320 LYS cc_start: 0.9182 (tttt) cc_final: 0.8909 (tptt) REVERT: I 215 LYS cc_start: 0.9288 (ttmm) cc_final: 0.8720 (ttmm) REVERT: I 320 LYS cc_start: 0.9168 (tttt) cc_final: 0.8900 (tptt) REVERT: J 320 LYS cc_start: 0.9184 (tttt) cc_final: 0.8908 (tptt) REVERT: K 78 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.9269 (pt) REVERT: K 178 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8903 (pp) REVERT: K 295 GLU cc_start: 0.8518 (tp30) cc_final: 0.8301 (tt0) REVERT: K 320 LYS cc_start: 0.9139 (tttt) cc_final: 0.8867 (tptt) REVERT: L 215 LYS cc_start: 0.9187 (ttmm) cc_final: 0.8954 (ttpp) REVERT: L 320 LYS cc_start: 0.9125 (tttt) cc_final: 0.8810 (tptt) outliers start: 79 outliers final: 35 residues processed: 423 average time/residue: 2.7439 time to fit residues: 1356.5438 Evaluate side-chains 387 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 348 time to evaluate : 3.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 267 LYS Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 11 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 350 optimal weight: 1.9990 chunk 371 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 332 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 31596 Z= 0.331 Angle : 0.766 15.722 42660 Z= 0.394 Chirality : 0.158 1.761 4668 Planarity : 0.004 0.042 5424 Dihedral : 4.819 19.699 4284 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.84 % Allowed : 15.36 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.52 (0.13), residues: 3912 helix: 0.02 (0.10), residues: 2304 sheet: -2.07 (0.20), residues: 408 loop : -2.50 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 198 HIS 0.005 0.002 HIS G 196 PHE 0.014 0.002 PHE J 288 TYR 0.014 0.001 TYR L 229 ARG 0.007 0.001 ARG E 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 378 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 GLU cc_start: 0.7985 (tp30) cc_final: 0.7635 (tp30) REVERT: C 320 LYS cc_start: 0.9217 (tttt) cc_final: 0.8939 (tptt) REVERT: D 227 GLU cc_start: 0.7994 (tp30) cc_final: 0.7642 (tp30) REVERT: D 320 LYS cc_start: 0.9253 (tttt) cc_final: 0.8984 (tptt) REVERT: E 178 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8833 (pp) REVERT: F 320 LYS cc_start: 0.9202 (tttt) cc_final: 0.8910 (tptt) REVERT: G 320 LYS cc_start: 0.9262 (tttt) cc_final: 0.9022 (tptt) REVERT: H 227 GLU cc_start: 0.8067 (tp30) cc_final: 0.7705 (tp30) REVERT: H 320 LYS cc_start: 0.9273 (tttt) cc_final: 0.9020 (tptt) REVERT: I 320 LYS cc_start: 0.9251 (tttt) cc_final: 0.8998 (tptt) REVERT: J 320 LYS cc_start: 0.9261 (tttt) cc_final: 0.9016 (tptt) REVERT: K 178 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8836 (pp) REVERT: K 320 LYS cc_start: 0.9246 (tttt) cc_final: 0.8998 (tptt) REVERT: L 227 GLU cc_start: 0.8236 (tp30) cc_final: 0.7928 (tp30) REVERT: L 320 LYS cc_start: 0.9237 (tttt) cc_final: 0.8960 (tptt) outliers start: 59 outliers final: 32 residues processed: 420 average time/residue: 2.7459 time to fit residues: 1348.3923 Evaluate side-chains 377 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 343 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 33 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 316 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 333 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 31596 Z= 0.307 Angle : 0.751 15.749 42660 Z= 0.384 Chirality : 0.158 1.762 4668 Planarity : 0.004 0.046 5424 Dihedral : 4.745 19.236 4284 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.28 % Allowed : 16.04 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.22 (0.13), residues: 3912 helix: 0.18 (0.10), residues: 2316 sheet: -1.82 (0.21), residues: 408 loop : -2.28 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 198 HIS 0.003 0.001 HIS K 140 PHE 0.013 0.001 PHE J 288 TYR 0.012 0.001 TYR F 229 ARG 0.008 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 367 time to evaluate : 3.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9098 (tpp) cc_final: 0.8668 (tpp) REVERT: A 227 GLU cc_start: 0.7952 (tp30) cc_final: 0.7659 (tp30) REVERT: B 178 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8853 (pp) REVERT: C 178 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8867 (pp) REVERT: C 320 LYS cc_start: 0.9272 (tttt) cc_final: 0.8998 (tptt) REVERT: D 178 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8804 (pp) REVERT: D 227 GLU cc_start: 0.7899 (tp30) cc_final: 0.7588 (tp30) REVERT: D 320 LYS cc_start: 0.9287 (tttt) cc_final: 0.9040 (tptt) REVERT: E 178 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8829 (pp) REVERT: E 227 GLU cc_start: 0.7947 (tp30) cc_final: 0.7685 (tp30) REVERT: F 178 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8843 (pp) REVERT: F 227 GLU cc_start: 0.8127 (tp30) cc_final: 0.7877 (tp30) REVERT: F 320 LYS cc_start: 0.9240 (tttt) cc_final: 0.8956 (tptt) REVERT: G 227 GLU cc_start: 0.8043 (tp30) cc_final: 0.7750 (tp30) REVERT: G 320 LYS cc_start: 0.9278 (tttt) cc_final: 0.9048 (tptt) REVERT: H 227 GLU cc_start: 0.8025 (tp30) cc_final: 0.7738 (tp30) REVERT: H 320 LYS cc_start: 0.9281 (tttt) cc_final: 0.9042 (tptt) REVERT: I 227 GLU cc_start: 0.8047 (tp30) cc_final: 0.7762 (tp30) REVERT: I 320 LYS cc_start: 0.9265 (tttt) cc_final: 0.9031 (tptt) REVERT: J 178 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8806 (pp) REVERT: J 227 GLU cc_start: 0.8138 (tp30) cc_final: 0.7870 (tp30) REVERT: J 320 LYS cc_start: 0.9283 (tttt) cc_final: 0.9037 (tptt) REVERT: K 178 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8823 (pp) REVERT: K 227 GLU cc_start: 0.8052 (tp30) cc_final: 0.7718 (tp30) REVERT: K 320 LYS cc_start: 0.9262 (tttt) cc_final: 0.9025 (tptt) REVERT: L 227 GLU cc_start: 0.8180 (tp30) cc_final: 0.7933 (tp30) REVERT: L 320 LYS cc_start: 0.9271 (tttt) cc_final: 0.9014 (tptt) outliers start: 73 outliers final: 39 residues processed: 422 average time/residue: 2.6668 time to fit residues: 1324.3993 Evaluate side-chains 389 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 343 time to evaluate : 3.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 33 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 4.9990 chunk 334 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 371 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 31596 Z= 0.295 Angle : 0.749 15.426 42660 Z= 0.382 Chirality : 0.157 1.763 4668 Planarity : 0.004 0.058 5424 Dihedral : 4.666 18.525 4284 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.78 % Allowed : 16.92 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.13), residues: 3912 helix: 0.28 (0.10), residues: 2316 sheet: -1.65 (0.22), residues: 408 loop : -2.13 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 198 HIS 0.005 0.002 HIS E 196 PHE 0.012 0.001 PHE J 288 TYR 0.013 0.001 TYR L 229 ARG 0.011 0.001 ARG K 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 375 time to evaluate : 3.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8790 (pp) REVERT: A 227 GLU cc_start: 0.7973 (tp30) cc_final: 0.7681 (tp30) REVERT: B 178 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8811 (pp) REVERT: B 233 GLU cc_start: 0.8161 (pm20) cc_final: 0.7904 (pm20) REVERT: C 178 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8809 (pp) REVERT: C 320 LYS cc_start: 0.9278 (tttt) cc_final: 0.9032 (tptt) REVERT: D 178 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8804 (pp) REVERT: D 227 GLU cc_start: 0.7959 (tp30) cc_final: 0.7693 (tp30) REVERT: D 320 LYS cc_start: 0.9293 (tttt) cc_final: 0.9077 (tptt) REVERT: E 34 MET cc_start: 0.9210 (tpp) cc_final: 0.8835 (tpp) REVERT: E 178 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8826 (pp) REVERT: E 227 GLU cc_start: 0.8005 (tp30) cc_final: 0.7744 (tp30) REVERT: F 178 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8806 (pp) REVERT: F 227 GLU cc_start: 0.8115 (tp30) cc_final: 0.7872 (tp30) REVERT: F 320 LYS cc_start: 0.9286 (tttt) cc_final: 0.9028 (tptt) REVERT: G 178 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8789 (pp) REVERT: G 227 GLU cc_start: 0.8070 (tp30) cc_final: 0.7813 (tp30) REVERT: G 320 LYS cc_start: 0.9303 (tttt) cc_final: 0.9088 (tptt) REVERT: H 227 GLU cc_start: 0.8049 (tp30) cc_final: 0.7780 (tp30) REVERT: H 320 LYS cc_start: 0.9309 (tttt) cc_final: 0.9090 (tptt) REVERT: I 227 GLU cc_start: 0.8088 (tp30) cc_final: 0.7836 (tp30) REVERT: I 320 LYS cc_start: 0.9312 (tttt) cc_final: 0.9087 (tptt) REVERT: J 178 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8800 (pp) REVERT: J 227 GLU cc_start: 0.8166 (tp30) cc_final: 0.7870 (tp30) REVERT: J 320 LYS cc_start: 0.9301 (tttt) cc_final: 0.9072 (tptt) REVERT: K 178 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8780 (pp) REVERT: K 227 GLU cc_start: 0.8049 (tp30) cc_final: 0.7768 (tp30) REVERT: K 320 LYS cc_start: 0.9281 (tttt) cc_final: 0.9060 (tptt) REVERT: L 178 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8785 (pp) REVERT: L 227 GLU cc_start: 0.8174 (tp30) cc_final: 0.7927 (tp30) REVERT: L 320 LYS cc_start: 0.9296 (tttt) cc_final: 0.9053 (tptt) outliers start: 89 outliers final: 37 residues processed: 443 average time/residue: 2.5692 time to fit residues: 1344.0116 Evaluate side-chains 397 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 350 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 178 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 271 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 370 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 225 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN C 25 ASN D 25 ASN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31596 Z= 0.260 Angle : 0.739 15.472 42660 Z= 0.373 Chirality : 0.157 1.751 4668 Planarity : 0.003 0.044 5424 Dihedral : 4.584 18.168 4284 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.90 % Allowed : 17.32 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.84 (0.13), residues: 3912 helix: 0.44 (0.10), residues: 2316 sheet: -1.61 (0.22), residues: 420 loop : -2.06 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 198 HIS 0.003 0.001 HIS G 140 PHE 0.011 0.001 PHE K 288 TYR 0.013 0.001 TYR F 229 ARG 0.006 0.001 ARG E 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 390 time to evaluate : 3.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8779 (pp) REVERT: A 227 GLU cc_start: 0.7854 (tp30) cc_final: 0.7574 (tp30) REVERT: B 178 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8805 (pp) REVERT: B 233 GLU cc_start: 0.8189 (pm20) cc_final: 0.7929 (pm20) REVERT: C 178 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8828 (pp) REVERT: C 320 LYS cc_start: 0.9293 (tttt) cc_final: 0.9045 (tptt) REVERT: D 178 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8800 (pp) REVERT: D 227 GLU cc_start: 0.7885 (tp30) cc_final: 0.7620 (tp30) REVERT: D 320 LYS cc_start: 0.9307 (tttt) cc_final: 0.9089 (tptt) REVERT: E 178 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8803 (pp) REVERT: F 178 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8788 (pp) REVERT: F 320 LYS cc_start: 0.9280 (tttt) cc_final: 0.9021 (tptt) REVERT: G 178 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8775 (pp) REVERT: G 320 LYS cc_start: 0.9315 (tttt) cc_final: 0.9108 (tptt) REVERT: H 178 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8779 (pp) REVERT: H 320 LYS cc_start: 0.9322 (tttt) cc_final: 0.9109 (tptt) REVERT: I 320 LYS cc_start: 0.9326 (tttt) cc_final: 0.9109 (tptt) REVERT: J 178 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8785 (pp) REVERT: J 320 LYS cc_start: 0.9311 (tttt) cc_final: 0.9093 (tptt) REVERT: K 178 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8759 (pp) REVERT: K 320 LYS cc_start: 0.9298 (tttt) cc_final: 0.9084 (tptt) REVERT: L 178 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8789 (pp) REVERT: L 320 LYS cc_start: 0.9296 (tttt) cc_final: 0.9062 (tptt) outliers start: 93 outliers final: 38 residues processed: 467 average time/residue: 2.5678 time to fit residues: 1431.5006 Evaluate side-chains 400 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 351 time to evaluate : 3.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 178 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 290 optimal weight: 10.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 GLN E 25 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 ASN H 25 ASN ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 25 ASN J 142 GLN K 25 ASN ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN L 142 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31596 Z= 0.227 Angle : 0.736 15.447 42660 Z= 0.369 Chirality : 0.157 1.750 4668 Planarity : 0.004 0.056 5424 Dihedral : 4.485 17.384 4284 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.40 % Allowed : 18.60 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.63 (0.13), residues: 3912 helix: 0.61 (0.11), residues: 2304 sheet: -1.41 (0.23), residues: 420 loop : -1.99 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 198 HIS 0.002 0.001 HIS G 140 PHE 0.009 0.001 PHE I 288 TYR 0.012 0.001 TYR L 229 ARG 0.013 0.001 ARG J 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 380 time to evaluate : 3.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9111 (tpp) cc_final: 0.8491 (mmm) REVERT: A 178 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8791 (pp) REVERT: B 178 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8781 (pp) REVERT: B 319 GLU cc_start: 0.8785 (tt0) cc_final: 0.8141 (tt0) REVERT: C 178 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8812 (pp) REVERT: C 320 LYS cc_start: 0.9294 (tttt) cc_final: 0.9049 (tptt) REVERT: D 178 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8791 (pp) REVERT: D 320 LYS cc_start: 0.9306 (tttt) cc_final: 0.9089 (tptt) REVERT: E 178 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8786 (pp) REVERT: F 178 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8785 (pp) REVERT: F 320 LYS cc_start: 0.9292 (tttt) cc_final: 0.9040 (tptt) REVERT: G 178 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8761 (pp) REVERT: G 320 LYS cc_start: 0.9322 (tttt) cc_final: 0.9116 (tptt) REVERT: H 178 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8787 (pp) REVERT: H 320 LYS cc_start: 0.9322 (tttt) cc_final: 0.9111 (tptt) REVERT: I 320 LYS cc_start: 0.9324 (tttt) cc_final: 0.9109 (tptt) REVERT: J 178 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8793 (pp) REVERT: J 215 LYS cc_start: 0.9152 (ttmm) cc_final: 0.8941 (ttmm) REVERT: J 320 LYS cc_start: 0.9314 (tttt) cc_final: 0.9100 (tptt) REVERT: K 178 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8761 (pp) REVERT: K 320 LYS cc_start: 0.9306 (tttt) cc_final: 0.9097 (tptt) REVERT: L 178 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8787 (pp) REVERT: L 320 LYS cc_start: 0.9290 (tttt) cc_final: 0.9057 (tptt) outliers start: 77 outliers final: 36 residues processed: 444 average time/residue: 2.6243 time to fit residues: 1386.1931 Evaluate side-chains 391 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 344 time to evaluate : 3.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 178 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 0.0570 chunk 354 optimal weight: 7.9990 chunk 323 optimal weight: 10.0000 chunk 344 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 150 optimal weight: 0.5980 chunk 270 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 311 optimal weight: 5.9990 chunk 326 optimal weight: 4.9990 chunk 343 optimal weight: 0.9990 overall best weight: 2.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 ASN ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31596 Z= 0.262 Angle : 0.749 15.522 42660 Z= 0.377 Chirality : 0.157 1.760 4668 Planarity : 0.004 0.047 5424 Dihedral : 4.442 17.030 4284 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.12 % Allowed : 19.85 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.13), residues: 3912 helix: 0.60 (0.11), residues: 2304 sheet: -1.25 (0.23), residues: 420 loop : -1.90 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 198 HIS 0.003 0.001 HIS G 140 PHE 0.011 0.001 PHE K 288 TYR 0.016 0.001 TYR F 51 ARG 0.008 0.001 ARG J 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 342 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9164 (tpp) cc_final: 0.8503 (mmm) REVERT: A 178 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8792 (pp) REVERT: B 178 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8784 (pp) REVERT: C 178 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8789 (pp) REVERT: C 320 LYS cc_start: 0.9314 (tttt) cc_final: 0.9086 (tptt) REVERT: D 178 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8792 (pp) REVERT: D 320 LYS cc_start: 0.9330 (tttt) cc_final: 0.9117 (tptt) REVERT: E 178 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8785 (pp) REVERT: F 178 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8776 (pp) REVERT: F 320 LYS cc_start: 0.9303 (tttt) cc_final: 0.9082 (tptt) REVERT: G 178 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8791 (pp) REVERT: G 320 LYS cc_start: 0.9338 (tttt) cc_final: 0.9133 (tptt) REVERT: H 178 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8768 (pp) REVERT: H 320 LYS cc_start: 0.9341 (tttt) cc_final: 0.9128 (tptt) REVERT: I 320 LYS cc_start: 0.9342 (tttt) cc_final: 0.9125 (tptt) REVERT: J 178 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8792 (pp) REVERT: J 320 LYS cc_start: 0.9333 (tttt) cc_final: 0.9126 (tptt) REVERT: K 34 MET cc_start: 0.9243 (tpp) cc_final: 0.8838 (mmm) REVERT: K 178 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8771 (pp) REVERT: K 320 LYS cc_start: 0.9323 (tttt) cc_final: 0.9116 (tptt) REVERT: L 178 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8780 (pp) REVERT: L 320 LYS cc_start: 0.9315 (tttt) cc_final: 0.9092 (tptt) outliers start: 68 outliers final: 35 residues processed: 397 average time/residue: 2.6269 time to fit residues: 1228.4341 Evaluate side-chains 383 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 337 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 194 SER Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 194 SER Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 6.9990 chunk 364 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 382 optimal weight: 1.9990 chunk 352 optimal weight: 9.9990 chunk 304 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 235 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31596 Z= 0.254 Angle : 0.745 15.512 42660 Z= 0.375 Chirality : 0.157 1.757 4668 Planarity : 0.004 0.047 5424 Dihedral : 4.401 16.598 4284 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.78 % Allowed : 20.32 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.45 (0.13), residues: 3912 helix: 0.67 (0.11), residues: 2304 sheet: -1.10 (0.24), residues: 420 loop : -1.82 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 198 HIS 0.003 0.001 HIS G 140 PHE 0.010 0.001 PHE B 288 TYR 0.013 0.001 TYR L 229 ARG 0.008 0.001 ARG L 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 346 time to evaluate : 3.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9169 (tpp) cc_final: 0.8515 (mmm) REVERT: A 178 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8783 (pp) REVERT: B 178 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8774 (pp) REVERT: C 178 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8791 (pp) REVERT: C 320 LYS cc_start: 0.9328 (tttt) cc_final: 0.9104 (tptt) REVERT: D 178 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8804 (pp) REVERT: D 320 LYS cc_start: 0.9343 (tttt) cc_final: 0.9130 (tptt) REVERT: E 178 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8782 (pp) REVERT: F 178 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8801 (pp) REVERT: F 320 LYS cc_start: 0.9315 (tttt) cc_final: 0.9099 (tptt) REVERT: G 178 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8784 (pp) REVERT: G 320 LYS cc_start: 0.9355 (tttt) cc_final: 0.9148 (tptt) REVERT: H 178 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8776 (pp) REVERT: H 320 LYS cc_start: 0.9358 (tttt) cc_final: 0.9146 (tptt) REVERT: I 320 LYS cc_start: 0.9346 (tttt) cc_final: 0.9132 (tptt) REVERT: J 178 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8792 (pp) REVERT: J 320 LYS cc_start: 0.9340 (tttt) cc_final: 0.9137 (tptt) REVERT: K 34 MET cc_start: 0.9260 (tpp) cc_final: 0.8823 (mmm) REVERT: K 178 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8766 (pp) REVERT: K 320 LYS cc_start: 0.9339 (tttt) cc_final: 0.9132 (tptt) REVERT: L 178 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8779 (pp) REVERT: L 320 LYS cc_start: 0.9325 (tttt) cc_final: 0.9105 (tptt) outliers start: 57 outliers final: 32 residues processed: 396 average time/residue: 2.7424 time to fit residues: 1286.5756 Evaluate side-chains 378 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 335 time to evaluate : 3.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 194 SER Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain I residue 11 ASP Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 194 SER Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 194 SER Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 2.9990 chunk 324 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 313 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.095336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.070716 restraints weight = 243141.060| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.62 r_work: 0.2909 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31596 Z= 0.302 Angle : 0.755 15.472 42660 Z= 0.384 Chirality : 0.157 1.778 4668 Planarity : 0.004 0.046 5424 Dihedral : 4.413 16.493 4284 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.56 % Allowed : 20.63 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.51 (0.13), residues: 3912 helix: 0.60 (0.10), residues: 2340 sheet: -1.02 (0.24), residues: 420 loop : -1.93 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 198 HIS 0.004 0.001 HIS I 140 PHE 0.013 0.001 PHE K 288 TYR 0.011 0.001 TYR F 229 ARG 0.009 0.001 ARG J 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20201.46 seconds wall clock time: 345 minutes 52.46 seconds (20752.46 seconds total)