Starting phenix.real_space_refine on Wed Feb 14 19:02:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpi_0747/02_2024/6kpi_0747.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpi_0747/02_2024/6kpi_0747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpi_0747/02_2024/6kpi_0747.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpi_0747/02_2024/6kpi_0747.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpi_0747/02_2024/6kpi_0747.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpi_0747/02_2024/6kpi_0747.pdb" } resolution = 2.43 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= 0.004 sd= 0.403 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 24 5.21 5 S 120 5.16 5 C 20004 2.51 5 N 5076 2.21 5 O 5760 1.98 5 H 31225 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 62209 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: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "C" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5180 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: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "G" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 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: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5184 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "L" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5180 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.85, per 1000 atoms: 0.32 Number of scatterers: 62209 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 24 11.99 O 5760 8.00 N 5076 7.00 C 20004 6.00 H 31225 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: 38.28 Conformation dependent library (CDL) restraints added in 4.6 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: 216 helices and 12 sheets defined 68.0% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 10 through 14 removed outlier: 3.858A pdb=" N LEU A 13 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 82 through 97 removed outlier: 3.554A pdb=" N VAL A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 133 through 141 removed outlier: 3.652A pdb=" N MET A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 Processing helix chain 'A' and resid 184 through 197 removed outlier: 4.066A pdb=" N LEU A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 218 removed outlier: 3.534A pdb=" N TYR A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 removed outlier: 3.559A pdb=" N ALA A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 247 through 253 removed outlier: 3.713A pdb=" N HIS A 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 268 through 285 removed outlier: 3.954A pdb=" N VAL A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.598A pdb=" N LYS A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.858A pdb=" N LEU B 13 " --> pdb=" O LEU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 48 through 57 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 82 through 97 removed outlier: 3.553A pdb=" N VAL B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) Proline residue: B 93 - end of helix Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 133 through 141 removed outlier: 3.652A pdb=" N MET B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 171 Processing helix chain 'B' and resid 184 through 197 removed outlier: 4.066A pdb=" N LEU B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 218 removed outlier: 3.534A pdb=" N TYR B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 218 " --> pdb=" O VAL B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.559A pdb=" N ALA B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 245 Processing helix chain 'B' and resid 247 through 253 removed outlier: 3.714A pdb=" N HIS B 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 268 through 285 removed outlier: 3.954A pdb=" N VAL B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.598A pdb=" N LYS B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'C' and resid 10 through 14 removed outlier: 3.859A pdb=" N LEU C 13 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 37 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 82 through 97 removed outlier: 3.553A pdb=" N VAL C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 133 through 141 removed outlier: 3.652A pdb=" N MET C 137 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 171 Processing helix chain 'C' and resid 184 through 197 removed outlier: 4.065A pdb=" N LEU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 218 removed outlier: 3.534A pdb=" N TYR C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 218 " --> pdb=" O VAL C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 229 removed outlier: 3.559A pdb=" N ALA C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 225 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 245 Processing helix chain 'C' and resid 247 through 253 removed outlier: 3.713A pdb=" N HIS C 252 " --> pdb=" O GLN C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 268 Processing helix chain 'C' and resid 268 through 285 removed outlier: 3.954A pdb=" N VAL C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.598A pdb=" N LYS C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 313 through 326 Processing helix chain 'D' and resid 10 through 14 removed outlier: 3.858A pdb=" N LEU D 13 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 37 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'D' and resid 82 through 97 removed outlier: 3.553A pdb=" N VAL D 86 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Proline residue: D 93 - end of helix Processing helix chain 'D' and resid 108 through 113 Processing helix chain 'D' and resid 133 through 141 removed outlier: 3.652A pdb=" N MET D 137 " --> pdb=" O GLY D 133 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 184 through 197 removed outlier: 4.067A pdb=" N LEU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.534A pdb=" N TYR D 217 " --> pdb=" O ALA D 213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY D 218 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 229 removed outlier: 3.559A pdb=" N ALA D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 245 Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.714A pdb=" N HIS D 252 " --> pdb=" O GLN D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 268 through 285 removed outlier: 3.954A pdb=" N VAL D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 removed outlier: 3.598A pdb=" N LYS D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 313 through 326 Processing helix chain 'E' and resid 10 through 14 removed outlier: 3.857A pdb=" N LEU E 13 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 37 Processing helix chain 'E' and resid 48 through 57 Processing helix chain 'E' and resid 63 through 71 Processing helix chain 'E' and resid 82 through 97 removed outlier: 3.554A pdb=" N VAL E 86 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Proline residue: E 93 - end of helix Processing helix chain 'E' and resid 108 through 113 Processing helix chain 'E' and resid 133 through 141 removed outlier: 3.652A pdb=" N MET E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 184 through 197 removed outlier: 4.066A pdb=" N LEU E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 218 removed outlier: 3.533A pdb=" N TYR E 217 " --> pdb=" O ALA E 213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY E 218 " --> pdb=" O VAL E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 229 removed outlier: 3.560A pdb=" N ALA E 224 " --> pdb=" O SER E 220 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU E 225 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU E 226 " --> pdb=" O GLU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 245 Processing helix chain 'E' and resid 247 through 253 removed outlier: 3.714A pdb=" N HIS E 252 " --> pdb=" O GLN E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 268 through 285 removed outlier: 3.955A pdb=" N VAL E 272 " --> pdb=" O TYR E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 299 removed outlier: 3.598A pdb=" N LYS E 290 " --> pdb=" O GLY E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 312 Processing helix chain 'E' and resid 313 through 326 Processing helix chain 'F' and resid 10 through 14 removed outlier: 3.859A pdb=" N LEU F 13 " --> pdb=" O LEU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 37 Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 63 through 71 Processing helix chain 'F' and resid 82 through 97 removed outlier: 3.554A pdb=" N VAL F 86 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Proline residue: F 93 - end of helix Processing helix chain 'F' and resid 108 through 113 Processing helix chain 'F' and resid 133 through 141 removed outlier: 3.652A pdb=" N MET F 137 " --> pdb=" O GLY F 133 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 184 through 197 removed outlier: 4.066A pdb=" N LEU F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 218 removed outlier: 3.534A pdb=" N TYR F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY F 218 " --> pdb=" O VAL F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 229 removed outlier: 3.560A pdb=" N ALA F 224 " --> pdb=" O SER F 220 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU F 226 " --> pdb=" O GLU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 245 Processing helix chain 'F' and resid 247 through 253 removed outlier: 3.713A pdb=" N HIS F 252 " --> pdb=" O GLN F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.954A pdb=" N VAL F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 299 removed outlier: 3.598A pdb=" N LYS F 290 " --> pdb=" O GLY F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 312 Processing helix chain 'F' and resid 313 through 326 Processing helix chain 'G' and resid 10 through 14 removed outlier: 3.858A pdb=" N LEU G 13 " --> pdb=" O LEU G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 37 Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 63 through 71 Processing helix chain 'G' and resid 82 through 97 removed outlier: 3.554A pdb=" N VAL G 86 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA G 92 " --> pdb=" O GLU G 88 " (cutoff:3.500A) Proline residue: G 93 - end of helix Processing helix chain 'G' and resid 108 through 113 Processing helix chain 'G' and resid 133 through 141 removed outlier: 3.652A pdb=" N MET G 137 " --> pdb=" O GLY G 133 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 171 Processing helix chain 'G' and resid 184 through 197 removed outlier: 4.066A pdb=" N LEU G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 218 removed outlier: 3.534A pdb=" N TYR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY G 218 " --> pdb=" O VAL G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 229 removed outlier: 3.560A pdb=" N ALA G 224 " --> pdb=" O SER G 220 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU G 225 " --> pdb=" O PRO G 221 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 245 Processing helix chain 'G' and resid 247 through 253 removed outlier: 3.713A pdb=" N HIS G 252 " --> pdb=" O GLN G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 268 Processing helix chain 'G' and resid 268 through 285 removed outlier: 3.954A pdb=" N VAL G 272 " --> pdb=" O TYR G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 299 removed outlier: 3.598A pdb=" N LYS G 290 " --> pdb=" O GLY G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 312 Processing helix chain 'G' and resid 313 through 326 Processing helix chain 'H' and resid 10 through 14 removed outlier: 3.858A pdb=" N LEU H 13 " --> pdb=" O LEU H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 37 Processing helix chain 'H' and resid 48 through 57 Processing helix chain 'H' and resid 63 through 71 Processing helix chain 'H' and resid 82 through 97 removed outlier: 3.553A pdb=" N VAL H 86 " --> pdb=" O VAL H 82 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Proline residue: H 93 - end of helix Processing helix chain 'H' and resid 108 through 113 Processing helix chain 'H' and resid 133 through 141 removed outlier: 3.652A pdb=" N MET H 137 " --> pdb=" O GLY H 133 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP H 138 " --> pdb=" O GLU H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 171 Processing helix chain 'H' and resid 184 through 197 removed outlier: 4.066A pdb=" N LEU H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 218 removed outlier: 3.534A pdb=" N TYR H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY H 218 " --> pdb=" O VAL H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 229 removed outlier: 3.560A pdb=" N ALA H 224 " --> pdb=" O SER H 220 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU H 225 " --> pdb=" O PRO H 221 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU H 226 " --> pdb=" O GLU H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 245 Processing helix chain 'H' and resid 247 through 253 removed outlier: 3.714A pdb=" N HIS H 252 " --> pdb=" O GLN H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 268 Processing helix chain 'H' and resid 268 through 285 removed outlier: 3.955A pdb=" N VAL H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 299 removed outlier: 3.598A pdb=" N LYS H 290 " --> pdb=" O GLY H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 312 Processing helix chain 'H' and resid 313 through 326 Processing helix chain 'I' and resid 10 through 14 removed outlier: 3.858A pdb=" N LEU I 13 " --> pdb=" O LEU I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 37 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 63 through 71 Processing helix chain 'I' and resid 82 through 97 removed outlier: 3.552A pdb=" N VAL I 86 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) Proline residue: I 93 - end of helix Processing helix chain 'I' and resid 108 through 113 Processing helix chain 'I' and resid 133 through 141 removed outlier: 3.652A pdb=" N MET I 137 " --> pdb=" O GLY I 133 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP I 138 " --> pdb=" O GLU I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 Processing helix chain 'I' and resid 184 through 197 removed outlier: 4.066A pdb=" N LEU I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 218 removed outlier: 3.533A pdb=" N TYR I 217 " --> pdb=" O ALA I 213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY I 218 " --> pdb=" O VAL I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 229 removed outlier: 3.559A pdb=" N ALA I 224 " --> pdb=" O SER I 220 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU I 225 " --> pdb=" O PRO I 221 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU I 226 " --> pdb=" O GLU I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 245 Processing helix chain 'I' and resid 247 through 253 removed outlier: 3.714A pdb=" N HIS I 252 " --> pdb=" O GLN I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 268 Processing helix chain 'I' and resid 268 through 285 removed outlier: 3.954A pdb=" N VAL I 272 " --> pdb=" O TYR I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 299 removed outlier: 3.598A pdb=" N LYS I 290 " --> pdb=" O GLY I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 312 Processing helix chain 'I' and resid 313 through 326 Processing helix chain 'J' and resid 10 through 14 removed outlier: 3.858A pdb=" N LEU J 13 " --> pdb=" O LEU J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 37 Processing helix chain 'J' and resid 48 through 57 Processing helix chain 'J' and resid 63 through 71 Processing helix chain 'J' and resid 82 through 97 removed outlier: 3.553A pdb=" N VAL J 86 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) Proline residue: J 93 - end of helix Processing helix chain 'J' and resid 108 through 113 Processing helix chain 'J' and resid 133 through 141 removed outlier: 3.652A pdb=" N MET J 137 " --> pdb=" O GLY J 133 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 171 Processing helix chain 'J' and resid 184 through 197 removed outlier: 4.066A pdb=" N LEU J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU J 195 " --> pdb=" O ASP J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 218 removed outlier: 3.533A pdb=" N TYR J 217 " --> pdb=" O ALA J 213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY J 218 " --> pdb=" O VAL J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 229 removed outlier: 3.560A pdb=" N ALA J 224 " --> pdb=" O SER J 220 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU J 225 " --> pdb=" O PRO J 221 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU J 226 " --> pdb=" O GLU J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 245 Processing helix chain 'J' and resid 247 through 253 removed outlier: 3.714A pdb=" N HIS J 252 " --> pdb=" O GLN J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 268 Processing helix chain 'J' and resid 268 through 285 removed outlier: 3.954A pdb=" N VAL J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 299 removed outlier: 3.597A pdb=" N LYS J 290 " --> pdb=" O GLY J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 312 Processing helix chain 'J' and resid 313 through 326 Processing helix chain 'K' and resid 10 through 14 removed outlier: 3.858A pdb=" N LEU K 13 " --> pdb=" O LEU K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 37 Processing helix chain 'K' and resid 48 through 57 Processing helix chain 'K' and resid 63 through 71 Processing helix chain 'K' and resid 82 through 97 removed outlier: 3.553A pdb=" N VAL K 86 " --> pdb=" O VAL K 82 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) Proline residue: K 93 - end of helix Processing helix chain 'K' and resid 108 through 113 Processing helix chain 'K' and resid 133 through 141 removed outlier: 3.652A pdb=" N MET K 137 " --> pdb=" O GLY K 133 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP K 138 " --> pdb=" O GLU K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 Processing helix chain 'K' and resid 184 through 197 removed outlier: 4.066A pdb=" N LEU K 190 " --> pdb=" O GLU K 186 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 218 removed outlier: 3.535A pdb=" N TYR K 217 " --> pdb=" O ALA K 213 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY K 218 " --> pdb=" O VAL K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 229 removed outlier: 3.560A pdb=" N ALA K 224 " --> pdb=" O SER K 220 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU K 225 " --> pdb=" O PRO K 221 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU K 226 " --> pdb=" O GLU K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 245 Processing helix chain 'K' and resid 247 through 253 removed outlier: 3.715A pdb=" N HIS K 252 " --> pdb=" O GLN K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 268 Processing helix chain 'K' and resid 268 through 285 removed outlier: 3.955A pdb=" N VAL K 272 " --> pdb=" O TYR K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 299 removed outlier: 3.597A pdb=" N LYS K 290 " --> pdb=" O GLY K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 312 Processing helix chain 'K' and resid 313 through 326 Processing helix chain 'L' and resid 10 through 14 removed outlier: 3.859A pdb=" N LEU L 13 " --> pdb=" O LEU L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 37 Processing helix chain 'L' and resid 48 through 57 Processing helix chain 'L' and resid 63 through 71 Processing helix chain 'L' and resid 82 through 97 removed outlier: 3.553A pdb=" N VAL L 86 " --> pdb=" O VAL L 82 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) Proline residue: L 93 - end of helix Processing helix chain 'L' and resid 108 through 113 Processing helix chain 'L' and resid 133 through 141 removed outlier: 3.652A pdb=" N MET L 137 " --> pdb=" O GLY L 133 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP L 138 " --> pdb=" O GLU L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 Processing helix chain 'L' and resid 184 through 197 removed outlier: 4.066A pdb=" N LEU L 190 " --> pdb=" O GLU L 186 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 218 removed outlier: 3.534A pdb=" N TYR L 217 " --> pdb=" O ALA L 213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY L 218 " --> pdb=" O VAL L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 229 removed outlier: 3.560A pdb=" N ALA L 224 " --> pdb=" O SER L 220 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU L 225 " --> pdb=" O PRO L 221 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU L 226 " --> pdb=" O GLU L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 245 Processing helix chain 'L' and resid 247 through 253 removed outlier: 3.714A pdb=" N HIS L 252 " --> pdb=" O GLN L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 268 Processing helix chain 'L' and resid 268 through 285 removed outlier: 3.954A pdb=" N VAL L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 299 removed outlier: 3.599A pdb=" N LYS L 290 " --> pdb=" O GLY L 286 " (cutoff:3.500A) 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 61 through 62 removed outlier: 8.800A pdb=" N TYR A 62 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL A 43 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE A 101 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE A 125 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 103 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL A 127 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE A 105 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR A 124 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 62 removed outlier: 8.801A pdb=" N TYR B 62 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL B 43 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE B 101 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE B 125 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 103 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL B 127 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE B 105 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR B 124 " --> pdb=" O LYS B 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 61 through 62 removed outlier: 8.801A pdb=" N TYR C 62 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL C 43 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 18 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLY C 44 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL C 20 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE C 101 " --> pdb=" O ASP C 123 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE C 125 " --> pdb=" O PHE C 101 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU C 103 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL C 127 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE C 105 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR C 124 " --> pdb=" O LYS C 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 61 through 62 removed outlier: 8.800A pdb=" N TYR D 62 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL D 43 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE D 18 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLY D 44 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL D 20 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE D 101 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE D 125 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU D 103 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL D 127 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE D 105 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR D 124 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 61 through 62 removed outlier: 8.801A pdb=" N TYR E 62 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL E 43 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE E 18 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLY E 44 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL E 20 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE E 101 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE E 125 " --> pdb=" O PHE E 101 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU E 103 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL E 127 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE E 105 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR E 124 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 61 through 62 removed outlier: 8.800A pdb=" N TYR F 62 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL F 43 " --> pdb=" O TYR F 62 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE F 18 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLY F 44 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL F 20 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE F 101 " --> pdb=" O ASP F 123 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE F 125 " --> pdb=" O PHE F 101 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU F 103 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL F 127 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE F 105 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR F 124 " --> pdb=" O LYS F 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 61 through 62 removed outlier: 8.801A pdb=" N TYR G 62 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL G 43 " --> pdb=" O TYR G 62 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE G 18 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLY G 44 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL G 20 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE G 101 " --> pdb=" O ASP G 123 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE G 125 " --> pdb=" O PHE G 101 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU G 103 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL G 127 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE G 105 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR G 124 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 61 through 62 removed outlier: 8.800A pdb=" N TYR H 62 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL H 43 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE H 18 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLY H 44 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL H 20 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE H 101 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE H 125 " --> pdb=" O PHE H 101 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU H 103 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL H 127 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE H 105 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR H 124 " --> pdb=" O LYS H 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 61 through 62 removed outlier: 8.801A pdb=" N TYR I 62 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL I 43 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE I 101 " --> pdb=" O ASP I 123 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE I 125 " --> pdb=" O PHE I 101 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU I 103 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL I 127 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE I 105 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR I 124 " --> pdb=" O LYS I 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 61 through 62 removed outlier: 8.800A pdb=" N TYR J 62 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL J 43 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE J 101 " --> pdb=" O ASP J 123 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE J 125 " --> pdb=" O PHE J 101 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU J 103 " --> pdb=" O ILE J 125 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL J 127 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE J 105 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR J 124 " --> pdb=" O LYS J 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 61 through 62 removed outlier: 8.801A pdb=" N TYR K 62 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL K 43 " --> pdb=" O TYR K 62 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE K 101 " --> pdb=" O ASP K 123 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE K 125 " --> pdb=" O PHE K 101 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU K 103 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL K 127 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE K 105 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR K 124 " --> pdb=" O LYS K 153 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 61 through 62 removed outlier: 8.801A pdb=" N TYR L 62 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL L 43 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE L 101 " --> pdb=" O ASP L 123 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE L 125 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU L 103 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL L 127 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE L 105 " --> pdb=" O VAL L 127 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR L 124 " --> pdb=" O LYS L 153 " (cutoff:3.500A) 1776 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: 19.85 Time building geometry restraints manager: 40.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 31211 1.03 - 1.22: 14 1.22 - 1.41: 13019 1.41 - 1.61: 18349 1.61 - 1.80: 228 Bond restraints: 62821 Sorted by residual: bond pdb=" CB SER I 121 " pdb=" HB3 SER I 121 " ideal model delta sigma weight residual 0.970 1.041 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CB SER E 121 " pdb=" HB3 SER E 121 " ideal model delta sigma weight residual 0.970 1.027 -0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" CA ASP K 65 " pdb=" HA ASP K 65 " ideal model delta sigma weight residual 0.970 0.928 0.042 2.00e-02 2.50e+03 4.31e+00 bond pdb=" CB GLU L 63 " pdb=" HB2 GLU L 63 " ideal model delta sigma weight residual 0.970 0.942 0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" OG SER K 121 " pdb=" HG SER K 121 " ideal model delta sigma weight residual 0.840 0.867 -0.027 2.00e-02 2.50e+03 1.84e+00 ... (remaining 62816 not shown) Histogram of bond angle deviations from ideal: 55.73 - 72.79: 79 72.79 - 89.85: 193 89.85 - 106.91: 1193 106.91 - 123.97: 108392 123.97 - 141.04: 4129 Bond angle restraints: 113986 Sorted by residual: angle pdb=" C LYS K 55 " pdb=" N LYS K 56 " pdb=" H LYS K 56 " ideal model delta sigma weight residual 124.93 65.72 59.21 3.00e+00 1.11e-01 3.90e+02 angle pdb=" CA LYS K 56 " pdb=" N LYS K 56 " pdb=" H LYS K 56 " ideal model delta sigma weight residual 114.63 55.73 58.90 3.00e+00 1.11e-01 3.85e+02 angle pdb=" CA ALA L 31 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 114.63 55.89 58.74 3.00e+00 1.11e-01 3.83e+02 angle pdb=" CA ALA K 31 " pdb=" N ALA K 31 " pdb=" H ALA K 31 " ideal model delta sigma weight residual 114.63 55.94 58.69 3.00e+00 1.11e-01 3.83e+02 angle pdb=" C GLN K 30 " pdb=" N ALA K 31 " pdb=" H ALA K 31 " ideal model delta sigma weight residual 124.93 66.46 58.47 3.00e+00 1.11e-01 3.80e+02 ... (remaining 113981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.17: 25019 14.17 - 28.35: 3147 28.35 - 42.52: 677 42.52 - 56.69: 333 56.69 - 70.86: 45 Dihedral angle restraints: 29221 sinusoidal: 15868 harmonic: 13353 Sorted by residual: dihedral pdb=" CA GLU L 63 " pdb=" C GLU L 63 " pdb=" N ILE L 64 " pdb=" CA ILE L 64 " ideal model delta harmonic sigma weight residual -180.00 -147.28 -32.72 0 5.00e+00 4.00e-02 4.28e+01 dihedral pdb=" CA GLU H 63 " pdb=" C GLU H 63 " pdb=" N ILE H 64 " pdb=" CA ILE H 64 " ideal model delta harmonic sigma weight residual 180.00 -147.28 -32.72 0 5.00e+00 4.00e-02 4.28e+01 dihedral pdb=" CA GLU J 63 " pdb=" C GLU J 63 " pdb=" N ILE J 64 " pdb=" CA ILE J 64 " ideal model delta harmonic sigma weight residual -180.00 -147.28 -32.72 0 5.00e+00 4.00e-02 4.28e+01 ... (remaining 29218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3846 0.068 - 0.137: 702 0.137 - 0.205: 48 0.205 - 0.274: 47 0.274 - 0.342: 25 Chirality restraints: 4668 Sorted by residual: chirality pdb=" CB VAL C 127 " pdb=" CA VAL C 127 " pdb=" CG1 VAL C 127 " pdb=" CG2 VAL C 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CB VAL D 127 " pdb=" CA VAL D 127 " pdb=" CG1 VAL D 127 " pdb=" CG2 VAL D 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB VAL K 127 " pdb=" CA VAL K 127 " pdb=" CG1 VAL K 127 " pdb=" CG2 VAL K 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 4665 not shown) Planarity restraints: 9208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR I 146 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO I 147 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO I 147 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 147 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR L 146 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO L 147 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO L 147 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 147 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 146 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO B 147 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 147 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 147 " -0.026 5.00e-02 4.00e+02 ... (remaining 9205 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 827 2.01 - 2.66: 89095 2.66 - 3.30: 176355 3.30 - 3.95: 224288 3.95 - 4.60: 369460 Nonbonded interactions: 860025 Sorted by model distance: nonbonded pdb=" H PHE K 59 " pdb=" HA PHE K 59 " model vdw 1.359 1.816 nonbonded pdb=" H GLY G 232 " pdb=" HA2 GLY G 232 " model vdw 1.426 1.816 nonbonded pdb=" H LYS E 159 " pdb=" HA LYS E 159 " model vdw 1.514 1.816 nonbonded pdb=" H LYS K 56 " pdb=" HA LYS K 56 " model vdw 1.518 1.816 nonbonded pdb=" H LYS J 159 " pdb=" HA LYS J 159 " model vdw 1.525 1.816 ... (remaining 860020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401 through 402)) selection = (chain 'B' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1 through 402)) selection = chain 'C' selection = (chain 'D' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401 through 402)) selection = (chain 'E' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401 through 402)) selection = (chain 'F' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1 through 402)) selection = (chain 'G' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1 through 402)) selection = (chain 'H' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401 through 402)) selection = (chain 'I' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401 through 402)) selection = (chain 'J' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401 through 402)) selection = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 329 or res \ id 401 through 402)) 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.660 Extract box with map and model: 11.230 Check model and map are aligned: 0.680 Set scattering table: 0.430 Process input model: 144.410 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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 : 0.008 0.040 31596 Z= 0.512 Angle : 0.675 6.687 42660 Z= 0.377 Chirality : 0.058 0.342 4668 Planarity : 0.004 0.047 5424 Dihedral : 11.986 55.000 11736 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -4.39 (0.10), residues: 3912 helix: -2.71 (0.08), residues: 2376 sheet: -2.56 (0.17), residues: 504 loop : -2.89 (0.14), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 198 HIS 0.004 0.001 HIS F 196 PHE 0.014 0.002 PHE L 303 TYR 0.010 0.001 TYR C 217 ARG 0.007 0.001 ARG J 70 *********************** 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 458 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 458 time to evaluate : 3.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 274 ARG cc_start: 0.7886 (ttm-80) cc_final: 0.7621 (mtm110) REVERT: D 239 ARG cc_start: 0.8623 (ttp-170) cc_final: 0.7728 (ttp80) REVERT: E 215 LYS cc_start: 0.8948 (mttt) cc_final: 0.8678 (mmtm) REVERT: E 239 ARG cc_start: 0.8617 (ttp-170) cc_final: 0.7707 (ttp80) REVERT: F 274 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7730 (mtm110) REVERT: I 215 LYS cc_start: 0.8957 (mttt) cc_final: 0.8749 (mmtp) REVERT: I 274 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7662 (mtm110) REVERT: K 239 ARG cc_start: 0.8644 (ttp-170) cc_final: 0.7717 (ttp80) REVERT: K 274 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7740 (mtm110) REVERT: K 281 LYS cc_start: 0.8849 (tttt) cc_final: 0.8648 (ttmm) REVERT: L 274 ARG cc_start: 0.8036 (ttm-80) cc_final: 0.7821 (mtm110) outliers start: 0 outliers final: 4 residues processed: 458 average time/residue: 3.3994 time to fit residues: 1783.0727 Evaluate side-chains 282 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 278 time to evaluate : 3.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain G residue 25 ASN Chi-restraints excluded: chain I residue 40 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.9990 chunk 291 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 1.9990 chunk 348 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 154 GLN A 278 ASN B 96 GLN B 154 GLN B 278 ASN C 96 GLN C 154 GLN C 278 ASN D 40 ASN D 96 GLN D 154 GLN D 278 ASN E 96 GLN E 154 GLN E 278 ASN F 96 GLN F 154 GLN F 278 ASN G 96 GLN G 154 GLN G 278 ASN H 96 GLN H 154 GLN H 278 ASN I 96 GLN I 154 GLN I 278 ASN J 96 GLN J 154 GLN J 278 ASN K 96 GLN K 154 GLN K 278 ASN L 96 GLN L 154 GLN L 278 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31596 Z= 0.254 Angle : 0.728 20.995 42660 Z= 0.381 Chirality : 0.124 1.684 4668 Planarity : 0.004 0.040 5424 Dihedral : 4.548 28.234 4292 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.50 % Allowed : 7.68 % Favored : 90.82 % Cbeta Deviations : 0.06 % 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: -1.84 (0.12), residues: 3912 helix: -0.55 (0.10), residues: 2400 sheet: -2.03 (0.17), residues: 504 loop : -2.01 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 198 HIS 0.004 0.001 HIS H 140 PHE 0.012 0.002 PHE I 303 TYR 0.010 0.001 TYR L 217 ARG 0.002 0.000 ARG E 239 *********************** 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 322 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 274 time to evaluate : 3.756 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: A 216 GLU cc_start: 0.7842 (mp0) cc_final: 0.7429 (mp0) REVERT: B 154 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: B 215 LYS cc_start: 0.8911 (mmtp) cc_final: 0.8670 (mtpp) REVERT: C 274 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7754 (mtm110) REVERT: C 308 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: D 216 GLU cc_start: 0.7680 (mp0) cc_final: 0.7116 (mp0) REVERT: E 216 GLU cc_start: 0.7809 (mp0) cc_final: 0.7235 (mp0) REVERT: F 131 MET cc_start: 0.7140 (mmm) cc_final: 0.6894 (mmp) REVERT: F 154 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8277 (tt0) REVERT: F 216 GLU cc_start: 0.8012 (mp0) cc_final: 0.7336 (mp0) REVERT: F 274 ARG cc_start: 0.8056 (ttm-80) cc_final: 0.7781 (mtm110) REVERT: G 239 ARG cc_start: 0.8767 (mtp85) cc_final: 0.7676 (ttp80) REVERT: H 215 LYS cc_start: 0.8902 (mmtp) cc_final: 0.8661 (mtpp) REVERT: I 243 GLU cc_start: 0.8251 (tp30) cc_final: 0.8043 (tm-30) REVERT: I 274 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7812 (mtm110) REVERT: J 154 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8245 (mt0) REVERT: J 239 ARG cc_start: 0.8767 (mtp85) cc_final: 0.7459 (ttp80) REVERT: K 215 LYS cc_start: 0.8888 (mmtm) cc_final: 0.8641 (mtpp) REVERT: K 274 ARG cc_start: 0.8070 (ttm-80) cc_final: 0.7801 (mtm110) REVERT: L 216 GLU cc_start: 0.8007 (mp0) cc_final: 0.7338 (mp0) REVERT: L 239 ARG cc_start: 0.8738 (mtp85) cc_final: 0.7612 (ttp-110) REVERT: L 274 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7848 (mtm110) outliers start: 48 outliers final: 5 residues processed: 305 average time/residue: 3.3868 time to fit residues: 1183.3446 Evaluate side-chains 239 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 230 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain F residue 154 GLN Chi-restraints excluded: chain G residue 25 ASN Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain L residue 25 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 290 optimal weight: 5.9990 chunk 237 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 349 optimal weight: 3.9990 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: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 96 GLN B 154 GLN C 96 GLN C 154 GLN D 96 GLN E 96 GLN F 96 GLN F 154 GLN G 96 GLN H 96 GLN H 154 GLN I 96 GLN J 96 GLN J 154 GLN K 96 GLN K 154 GLN L 96 GLN L 154 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 31596 Z= 0.465 Angle : 0.767 21.196 42660 Z= 0.408 Chirality : 0.127 1.794 4668 Planarity : 0.004 0.037 5424 Dihedral : 4.446 28.376 4286 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.19 % Allowed : 8.77 % Favored : 90.04 % Cbeta Deviations : 0.06 % 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: -0.85 (0.12), residues: 3912 helix: 0.04 (0.10), residues: 2424 sheet: -0.56 (0.23), residues: 384 loop : -1.71 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 198 HIS 0.009 0.003 HIS L 196 PHE 0.016 0.002 PHE I 303 TYR 0.013 0.001 TYR J 300 ARG 0.004 0.000 ARG L 239 *********************** 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 293 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 255 time to evaluate : 3.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8882 (m-30) REVERT: C 274 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7952 (mtm110) REVERT: C 308 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: F 274 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7934 (mtm110) REVERT: I 274 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7994 (mtm110) REVERT: K 274 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7925 (mtm110) REVERT: L 215 LYS cc_start: 0.8800 (mttm) cc_final: 0.8482 (mtpp) REVERT: L 274 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7991 (mtm110) outliers start: 38 outliers final: 14 residues processed: 277 average time/residue: 3.3086 time to fit residues: 1054.6456 Evaluate side-chains 246 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 230 time to evaluate : 3.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain L residue 25 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 2.9990 chunk 262 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 234 optimal weight: 0.6980 chunk 350 optimal weight: 2.9990 chunk 371 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 332 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 154 GLN B 96 GLN C 96 GLN C 154 GLN D 96 GLN D 154 GLN E 96 GLN F 96 GLN F 154 GLN G 96 GLN G 154 GLN H 96 GLN H 154 GLN I 96 GLN J 96 GLN K 96 GLN K 154 GLN L 96 GLN L 154 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31596 Z= 0.222 Angle : 0.696 22.463 42660 Z= 0.360 Chirality : 0.128 1.735 4668 Planarity : 0.003 0.036 5424 Dihedral : 4.207 25.773 4284 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.66 % Allowed : 9.43 % Favored : 89.92 % Cbeta Deviations : 0.06 % 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: -0.05 (0.13), residues: 3912 helix: 0.62 (0.10), residues: 2412 sheet: -0.07 (0.24), residues: 384 loop : -1.29 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 198 HIS 0.003 0.001 HIS L 140 PHE 0.012 0.001 PHE I 303 TYR 0.009 0.001 TYR J 300 ARG 0.002 0.000 ARG L 239 *********************** 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 283 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 262 time to evaluate : 3.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 274 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7921 (mtm110) REVERT: C 308 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: F 274 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7904 (mtm110) REVERT: I 274 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7919 (mtm110) REVERT: K 274 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7916 (mtm110) REVERT: L 274 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7963 (mtm110) outliers start: 21 outliers final: 2 residues processed: 274 average time/residue: 3.2076 time to fit residues: 1025.1920 Evaluate side-chains 252 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 249 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain I residue 99 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 316 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 chunk 333 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 154 GLN B 96 GLN C 96 GLN C 154 GLN D 96 GLN D 154 GLN E 96 GLN F 96 GLN G 96 GLN G 154 GLN H 96 GLN H 154 GLN I 96 GLN J 96 GLN K 96 GLN K 154 GLN L 96 GLN L 154 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 31596 Z= 0.347 Angle : 0.722 21.866 42660 Z= 0.375 Chirality : 0.129 1.733 4668 Planarity : 0.003 0.034 5424 Dihedral : 4.159 24.418 4284 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.72 % Allowed : 9.93 % Favored : 89.36 % Cbeta Deviations : 0.03 % 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: 0.30 (0.13), residues: 3912 helix: 0.84 (0.10), residues: 2412 sheet: 0.23 (0.25), residues: 408 loop : -1.13 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 198 HIS 0.005 0.002 HIS H 196 PHE 0.014 0.002 PHE I 303 TYR 0.010 0.001 TYR J 300 ARG 0.003 0.000 ARG F 130 *********************** 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 267 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 244 time to evaluate : 3.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 274 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.8007 (mtm110) REVERT: C 308 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: F 154 GLN cc_start: 0.8531 (tt0) cc_final: 0.8103 (mt0) REVERT: F 274 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7993 (mtm110) REVERT: I 274 ARG cc_start: 0.8185 (ttm-80) cc_final: 0.7978 (mtm110) REVERT: K 274 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7983 (mtm110) outliers start: 23 outliers final: 8 residues processed: 257 average time/residue: 3.1218 time to fit residues: 929.8449 Evaluate side-chains 244 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 235 time to evaluate : 3.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain L residue 25 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 2.9990 chunk 334 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 371 optimal weight: 3.9990 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN B 154 GLN C 96 GLN C 154 GLN D 154 GLN E 96 GLN F 96 GLN G 96 GLN G 154 GLN H 96 GLN H 154 GLN I 96 GLN J 154 GLN K 96 GLN K 154 GLN L 96 GLN L 154 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 31596 Z= 0.305 Angle : 0.711 21.326 42660 Z= 0.367 Chirality : 0.129 1.735 4668 Planarity : 0.003 0.032 5424 Dihedral : 4.119 23.866 4284 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.62 % Allowed : 10.24 % Favored : 89.14 % Cbeta Deviations : 0.03 % 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: 0.64 (0.13), residues: 3912 helix: 1.07 (0.10), residues: 2424 sheet: 0.42 (0.25), residues: 408 loop : -0.92 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 198 HIS 0.004 0.001 HIS L 196 PHE 0.013 0.002 PHE I 303 TYR 0.010 0.001 TYR J 300 ARG 0.002 0.000 ARG I 130 *********************** 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 256 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 236 time to evaluate : 3.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 274 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7996 (mtm110) REVERT: C 308 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: F 154 GLN cc_start: 0.8530 (tt0) cc_final: 0.8132 (mt0) REVERT: K 274 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7977 (mtm110) outliers start: 20 outliers final: 6 residues processed: 246 average time/residue: 3.1454 time to fit residues: 903.4762 Evaluate side-chains 241 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 234 time to evaluate : 3.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain J residue 95 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 0.2980 chunk 41 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 271 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 312 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 370 optimal weight: 0.7980 chunk 231 optimal weight: 0.8980 chunk 225 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN B 154 GLN C 96 GLN C 154 GLN D 96 GLN D 154 GLN E 96 GLN G 96 GLN G 154 GLN H 154 GLN J 154 GLN K 96 GLN K 154 GLN L 154 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31596 Z= 0.215 Angle : 0.688 21.738 42660 Z= 0.352 Chirality : 0.129 1.730 4668 Planarity : 0.003 0.031 5424 Dihedral : 3.997 22.765 4284 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.56 % Allowed : 10.36 % Favored : 89.08 % Cbeta Deviations : 0.03 % 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: 0.99 (0.13), residues: 3912 helix: 1.36 (0.10), residues: 2448 sheet: 0.55 (0.25), residues: 408 loop : -0.87 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 198 HIS 0.003 0.001 HIS B 196 PHE 0.010 0.001 PHE I 303 TYR 0.008 0.001 TYR J 300 ARG 0.001 0.000 ARG A 130 *********************** 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 272 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 254 time to evaluate : 3.741 Fit side-chains REVERT: C 308 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: F 154 GLN cc_start: 0.8499 (tt0) cc_final: 0.8098 (mt0) outliers start: 18 outliers final: 8 residues processed: 263 average time/residue: 3.0107 time to fit residues: 931.9331 Evaluate side-chains 257 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 248 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain L residue 95 LEU 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: 3.9990 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 290 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: A 154 GLN B 96 GLN C 154 GLN D 96 GLN E 96 GLN E 154 GLN F 96 GLN G 96 GLN G 154 GLN H 96 GLN H 154 GLN I 96 GLN J 96 GLN K 96 GLN K 154 GLN L 96 GLN L 154 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 31596 Z= 0.279 Angle : 0.708 21.599 42660 Z= 0.363 Chirality : 0.129 1.733 4668 Planarity : 0.003 0.031 5424 Dihedral : 3.990 22.790 4284 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.81 % Allowed : 10.36 % Favored : 88.83 % Cbeta Deviations : 0.03 % 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: 1.01 (0.13), residues: 3912 helix: 1.43 (0.10), residues: 2448 sheet: -0.29 (0.23), residues: 516 loop : -0.62 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 198 HIS 0.004 0.001 HIS D 196 PHE 0.013 0.002 PHE I 303 TYR 0.010 0.001 TYR J 300 ARG 0.002 0.000 ARG I 130 *********************** 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 277 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 251 time to evaluate : 3.762 Fit side-chains REVERT: C 308 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: F 154 GLN cc_start: 0.8527 (tt0) cc_final: 0.8151 (mt0) outliers start: 26 outliers final: 12 residues processed: 268 average time/residue: 2.8152 time to fit residues: 888.3251 Evaluate side-chains 257 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 244 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 25 ASN Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain L residue 25 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 6.9990 chunk 354 optimal weight: 5.9990 chunk 323 optimal weight: 4.9990 chunk 344 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 270 optimal weight: 6.9990 chunk 105 optimal weight: 0.0030 chunk 311 optimal weight: 10.0000 chunk 326 optimal weight: 2.9990 chunk 343 optimal weight: 0.7980 overall best weight: 2.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 154 GLN B 96 GLN C 154 GLN D 96 GLN E 96 GLN E 154 GLN G 96 GLN G 154 GLN H 154 GLN I 154 GLN J 96 GLN K 96 GLN K 154 GLN L 96 GLN L 154 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 31596 Z= 0.258 Angle : 0.708 21.579 42660 Z= 0.362 Chirality : 0.129 1.732 4668 Planarity : 0.003 0.029 5424 Dihedral : 3.962 22.617 4284 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.62 % Allowed : 10.14 % Favored : 89.23 % Cbeta Deviations : 0.03 % 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: 1.14 (0.13), residues: 3912 helix: 1.54 (0.10), residues: 2448 sheet: -0.25 (0.23), residues: 516 loop : -0.58 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 198 HIS 0.003 0.001 HIS G 196 PHE 0.012 0.002 PHE I 303 TYR 0.009 0.001 TYR J 300 ARG 0.002 0.000 ARG A 130 *********************** 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 276 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 256 time to evaluate : 3.749 Fit side-chains REVERT: C 308 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: F 154 GLN cc_start: 0.8502 (tt0) cc_final: 0.8166 (mt0) REVERT: K 216 GLU cc_start: 0.8262 (mp0) cc_final: 0.7972 (mp0) outliers start: 20 outliers final: 12 residues processed: 266 average time/residue: 2.8678 time to fit residues: 899.6988 Evaluate side-chains 255 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 242 time to evaluate : 3.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain L residue 95 LEU 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: 4.9990 chunk 222 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 253 optimal weight: 3.9990 chunk 382 optimal weight: 1.9990 chunk 352 optimal weight: 3.9990 chunk 304 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 154 GLN B 96 GLN C 96 GLN C 154 GLN D 96 GLN E 96 GLN E 154 GLN F 96 GLN G 96 GLN G 154 GLN H 96 GLN H 154 GLN I 154 GLN J 96 GLN K 96 GLN K 154 GLN L 96 GLN L 154 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 31596 Z= 0.280 Angle : 0.721 21.273 42660 Z= 0.368 Chirality : 0.129 1.732 4668 Planarity : 0.003 0.027 5424 Dihedral : 3.966 22.464 4284 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.62 % Allowed : 10.21 % Favored : 89.17 % Cbeta Deviations : 0.06 % 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: 1.16 (0.13), residues: 3912 helix: 1.54 (0.10), residues: 2448 sheet: -0.21 (0.23), residues: 516 loop : -0.57 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 198 HIS 0.004 0.001 HIS J 196 PHE 0.012 0.002 PHE I 303 TYR 0.009 0.001 TYR J 300 ARG 0.002 0.000 ARG E 130 ********************** 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 266 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 246 time to evaluate : 3.713 Fit side-chains REVERT: C 308 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: F 154 GLN cc_start: 0.8504 (tt0) cc_final: 0.8169 (mt0) REVERT: K 216 GLU cc_start: 0.8289 (mp0) cc_final: 0.7994 (mp0) REVERT: L 216 GLU cc_start: 0.8307 (mp0) cc_final: 0.8002 (mp0) outliers start: 20 outliers final: 15 residues processed: 255 average time/residue: 3.0904 time to fit residues: 935.5515 Evaluate side-chains 256 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 240 time to evaluate : 3.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain L residue 25 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 1.9990 chunk 324 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 0.0000 chunk 127 optimal weight: 4.9990 chunk 313 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 154 GLN B 96 GLN C 96 GLN C 154 GLN D 96 GLN D 154 GLN E 96 GLN E 154 GLN F 96 GLN G 96 GLN G 154 GLN H 96 GLN H 154 GLN I 154 GLN J 96 GLN K 96 GLN K 154 GLN L 96 GLN L 154 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.077856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.053588 restraints weight = 203331.233| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 3.06 r_work: 0.2495 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2357 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 31596 Z= 0.234 Angle : 0.709 21.498 42660 Z= 0.361 Chirality : 0.129 1.729 4668 Planarity : 0.003 0.026 5424 Dihedral : 3.928 22.183 4284 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.62 % Allowed : 10.33 % Favored : 89.04 % Cbeta Deviations : 0.06 % 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: 1.27 (0.14), residues: 3912 helix: 1.63 (0.10), residues: 2448 sheet: -0.18 (0.23), residues: 516 loop : -0.52 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 198 HIS 0.003 0.001 HIS A 196 PHE 0.011 0.001 PHE I 303 TYR 0.009 0.001 TYR B 300 ARG 0.001 0.000 ARG G 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17040.39 seconds wall clock time: 293 minutes 30.45 seconds (17610.45 seconds total)