Starting phenix.real_space_refine on Wed Feb 14 18:44:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq8_0751/02_2024/6kq8_0751.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq8_0751/02_2024/6kq8_0751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq8_0751/02_2024/6kq8_0751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq8_0751/02_2024/6kq8_0751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq8_0751/02_2024/6kq8_0751.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq8_0751/02_2024/6kq8_0751.pdb" } resolution = 3.0 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= 0.008 sd= 0.312 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 12 5.21 5 S 120 5.16 5 C 20004 2.51 5 N 5076 2.21 5 O 5760 1.98 5 H 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 ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 101": "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 ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 63": "OE1" <-> "OE2" Residue "I ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 62197 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.02, per 1000 atoms: 0.34 Number of scatterers: 62197 At special positions: 0 Unit cell: (145.32, 144.48, 144.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 Mg 12 11.99 O 5760 8.00 N 5076 7.00 C 20004 6.00 H 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: 37.64 Conformation dependent library (CDL) restraints added in 5.5 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: 222 helices and 12 sheets defined 66.2% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 10 through 14 removed outlier: 3.661A pdb=" N LEU A 13 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 37 removed outlier: 3.786A pdb=" N MET A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 57 removed outlier: 3.874A pdb=" N LYS A 55 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 70 removed outlier: 3.638A pdb=" N ARG A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 90 through 97 removed outlier: 3.961A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 134 through 141 removed outlier: 3.501A 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 194 removed outlier: 4.576A pdb=" N LEU A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 218 removed outlier: 3.551A pdb=" N ILE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 removed outlier: 3.657A pdb=" N ALA A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 4.422A 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 Processing helix chain 'A' and resid 254 through 285 removed outlier: 3.817A pdb=" N GLN A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASP A 270 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.549A pdb=" N LYS A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 removed outlier: 3.672A pdb=" N THR A 311 " --> pdb=" O TRP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 326 removed outlier: 3.508A pdb=" N LEU A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.683A pdb=" N LEU B 13 " --> pdb=" O LEU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 35 Processing helix chain 'B' and resid 48 through 57 removed outlier: 3.620A pdb=" N LYS B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 70 removed outlier: 3.518A pdb=" N ARG B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 90 through 97 removed outlier: 4.139A pdb=" N VAL B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 134 through 141 removed outlier: 3.537A 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 194 removed outlier: 4.529A pdb=" N LEU B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 218 removed outlier: 3.562A pdb=" N ILE B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.631A pdb=" N ALA B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 245 removed outlier: 3.536A pdb=" N GLU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 268 through 285 removed outlier: 4.142A pdb=" N VAL B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.631A pdb=" N LYS B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.693A pdb=" N THR B 311 " --> pdb=" O TRP B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 327 removed outlier: 3.925A pdb=" N LYS B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 14 removed outlier: 3.775A pdb=" N LEU C 13 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 35 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 63 through 70 removed outlier: 3.642A pdb=" N ARG C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.916A pdb=" N VAL C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 133 through 141 removed outlier: 4.219A pdb=" N MET C 137 " --> pdb=" O GLY C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 171 Processing helix chain 'C' and resid 184 through 194 removed outlier: 4.512A pdb=" N LEU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 218 removed outlier: 3.624A pdb=" N ILE C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 229 removed outlier: 3.658A pdb=" N ALA C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU C 225 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 245 removed outlier: 3.571A pdb=" N GLU C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 254 through 285 removed outlier: 6.108A pdb=" N ASP C 270 " --> pdb=" O PHE C 266 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL C 271 " --> pdb=" O LYS C 267 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 297 removed outlier: 3.680A pdb=" N LYS C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 312 removed outlier: 3.732A pdb=" N THR C 311 " --> pdb=" O TRP C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 326 removed outlier: 3.659A pdb=" N LYS C 317 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 14 removed outlier: 3.778A pdb=" N LEU D 13 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 35 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 63 through 70 removed outlier: 3.517A pdb=" N ARG D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.890A pdb=" N VAL D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY D 97 " --> pdb=" O PRO D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 113 Processing helix chain 'D' and resid 133 through 141 removed outlier: 3.934A pdb=" N MET D 137 " --> pdb=" O GLY D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 184 through 194 removed outlier: 4.517A pdb=" N LEU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.616A pdb=" N ILE D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR D 217 " --> pdb=" O ALA D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 229 removed outlier: 3.651A pdb=" N ALA D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 245 removed outlier: 3.631A pdb=" N GLU D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 254 through 285 removed outlier: 6.113A pdb=" N ASP D 270 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL D 271 " --> pdb=" O LYS D 267 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 removed outlier: 3.551A pdb=" N LYS D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 removed outlier: 3.753A pdb=" N THR D 311 " --> pdb=" O TRP D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 326 removed outlier: 3.736A pdb=" N LYS D 317 " --> pdb=" O SER D 313 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 14 removed outlier: 3.583A pdb=" N LEU E 13 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 35 Processing helix chain 'E' and resid 48 through 57 Processing helix chain 'E' and resid 63 through 70 removed outlier: 3.632A pdb=" N ARG E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 90 through 97 removed outlier: 4.024A pdb=" N VAL E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY E 97 " --> pdb=" O PRO E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 Processing helix chain 'E' and resid 134 through 141 removed outlier: 3.675A 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 194 removed outlier: 4.491A pdb=" N LEU E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 218 removed outlier: 3.635A pdb=" N ILE E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR E 217 " --> pdb=" O ALA E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 229 removed outlier: 3.681A pdb=" N ALA E 224 " --> pdb=" O SER E 220 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU E 225 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU E 226 " --> pdb=" O GLU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 245 removed outlier: 3.599A pdb=" N GLU E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 253 Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 268 through 285 removed outlier: 3.913A pdb=" N VAL E 272 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP E 285 " --> pdb=" O LYS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 297 removed outlier: 3.600A pdb=" N LYS E 290 " --> pdb=" O GLY E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 312 removed outlier: 3.642A pdb=" N THR E 311 " --> pdb=" O TRP E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 326 removed outlier: 3.732A pdb=" N LYS E 317 " --> pdb=" O SER E 313 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 14 removed outlier: 3.760A pdb=" N LEU F 13 " --> pdb=" O LEU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 37 removed outlier: 3.809A pdb=" N MET F 34 " --> pdb=" O GLN F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 65 through 70 removed outlier: 3.633A pdb=" N ARG F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG F 70 " --> pdb=" O GLU F 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 65 through 70' Processing helix chain 'F' and resid 82 through 90 Processing helix chain 'F' and resid 90 through 97 removed outlier: 3.897A pdb=" N VAL F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY F 97 " --> pdb=" O PRO F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 113 Processing helix chain 'F' and resid 134 through 141 removed outlier: 3.726A 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: 4.486A pdb=" N LEU F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 218 removed outlier: 3.657A pdb=" N ILE F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 229 removed outlier: 3.653A pdb=" N ALA F 224 " --> pdb=" O SER F 220 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 4.495A 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 Processing helix chain 'F' and resid 254 through 268 removed outlier: 3.735A pdb=" N GLN F 258 " --> pdb=" O SER F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.891A pdb=" N VAL F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP F 285 " --> pdb=" O LYS F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 299 removed outlier: 3.544A pdb=" N LYS F 290 " --> pdb=" O GLY F 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN F 297 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 312 removed outlier: 3.663A pdb=" N THR F 311 " --> pdb=" O TRP F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 326 removed outlier: 3.539A pdb=" N LEU F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 14 removed outlier: 3.702A pdb=" N LEU G 13 " --> pdb=" O LEU G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 37 removed outlier: 3.932A pdb=" N VAL G 29 " --> pdb=" O ASN G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.659A pdb=" N LYS G 55 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 70 removed outlier: 3.613A pdb=" N ALA G 67 " --> pdb=" O GLU G 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG G 69 " --> pdb=" O ASP G 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG G 70 " --> pdb=" O GLU G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.925A pdb=" N VAL G 94 " --> pdb=" O LYS G 90 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY G 97 " --> pdb=" O PRO G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 113 Processing helix chain 'G' and resid 136 through 141 removed outlier: 3.503A pdb=" N LYS G 141 " --> pdb=" O MET G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 171 Processing helix chain 'G' and resid 184 through 194 removed outlier: 4.529A pdb=" N LEU G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 218 removed outlier: 3.566A pdb=" N ILE G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 229 removed outlier: 3.646A pdb=" N ALA G 224 " --> pdb=" O SER G 220 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU G 225 " --> pdb=" O PRO G 221 " (cutoff:3.500A) removed outlier: 4.517A 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 Processing helix chain 'G' and resid 254 through 268 Processing helix chain 'G' and resid 268 through 285 removed outlier: 4.235A pdb=" N VAL G 272 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP G 285 " --> pdb=" O LYS G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 299 removed outlier: 3.595A pdb=" N LYS G 290 " --> pdb=" O GLY G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 312 removed outlier: 3.646A pdb=" N THR G 311 " --> pdb=" O TRP G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 326 removed outlier: 3.607A pdb=" N LYS G 317 " --> pdb=" O SER G 313 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 14 removed outlier: 3.653A pdb=" N LEU H 13 " --> pdb=" O LEU H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 37 removed outlier: 3.567A pdb=" N VAL H 29 " --> pdb=" O ASN H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 57 Processing helix chain 'H' and resid 63 through 71 removed outlier: 3.544A pdb=" N SER H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 90 Processing helix chain 'H' and resid 90 through 97 removed outlier: 4.131A pdb=" N VAL H 94 " --> pdb=" O LYS H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 Processing helix chain 'H' and resid 134 through 141 removed outlier: 3.538A 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 194 removed outlier: 4.505A pdb=" N LEU H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 218 removed outlier: 3.562A pdb=" N ILE H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 229 removed outlier: 3.654A pdb=" N ALA H 224 " --> pdb=" O SER H 220 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU H 225 " --> pdb=" O PRO H 221 " (cutoff:3.500A) removed outlier: 4.477A 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 Processing helix chain 'H' and resid 254 through 285 removed outlier: 6.147A pdb=" N ASP H 270 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL H 271 " --> pdb=" O LYS H 267 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 299 removed outlier: 3.696A pdb=" N LYS H 290 " --> pdb=" O GLY H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 312 removed outlier: 3.681A pdb=" N THR H 311 " --> pdb=" O TRP H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 326 Processing helix chain 'I' and resid 24 through 37 removed outlier: 3.618A pdb=" N ARG I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL I 29 " --> pdb=" O ASN I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 63 through 71 removed outlier: 3.637A pdb=" N ARG I 69 " --> pdb=" O ASP I 65 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG I 70 " --> pdb=" O GLU I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 90 through 97 removed outlier: 3.957A pdb=" N VAL I 94 " --> pdb=" O LYS I 90 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY I 97 " --> pdb=" O PRO I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 113 Processing helix chain 'I' and resid 134 through 141 removed outlier: 4.244A 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 194 removed outlier: 4.541A pdb=" N LEU I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 218 removed outlier: 3.610A pdb=" N ILE I 201 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR I 217 " --> pdb=" O ALA I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 229 removed outlier: 3.616A pdb=" N ALA I 224 " --> pdb=" O SER I 220 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU I 225 " --> pdb=" O PRO I 221 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU I 226 " --> pdb=" O GLU I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 245 removed outlier: 3.682A pdb=" N GLU I 236 " --> pdb=" O GLY I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 253 Processing helix chain 'I' and resid 254 through 268 Processing helix chain 'I' and resid 268 through 285 removed outlier: 3.911A pdb=" N VAL I 272 " --> pdb=" O TYR I 268 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP I 285 " --> pdb=" O LYS I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 299 removed outlier: 3.767A pdb=" N GLN I 297 " --> pdb=" O SER I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 312 removed outlier: 3.659A pdb=" N THR I 311 " --> pdb=" O TRP I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 326 removed outlier: 3.636A pdb=" N LYS I 317 " --> pdb=" O SER I 313 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU I 325 " --> pdb=" O GLU I 321 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 35 removed outlier: 3.517A pdb=" N VAL J 29 " --> pdb=" O ASN J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 57 Processing helix chain 'J' and resid 63 through 71 removed outlier: 3.656A pdb=" N ARG J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG J 70 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 90 Processing helix chain 'J' and resid 90 through 97 removed outlier: 3.948A pdb=" N VAL J 94 " --> pdb=" O LYS J 90 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY J 97 " --> pdb=" O PRO J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 113 Processing helix chain 'J' and resid 134 through 141 removed outlier: 4.044A 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 194 removed outlier: 4.579A pdb=" N LEU J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 218 removed outlier: 3.622A pdb=" N ILE J 201 " --> pdb=" O THR J 197 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR J 217 " --> pdb=" O ALA J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 229 removed outlier: 3.630A pdb=" N ALA J 224 " --> pdb=" O SER J 220 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU J 225 " --> pdb=" O PRO J 221 " (cutoff:3.500A) removed outlier: 4.489A 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 Processing helix chain 'J' and resid 254 through 268 Processing helix chain 'J' and resid 268 through 285 removed outlier: 3.901A pdb=" N VAL J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP J 285 " --> pdb=" O LYS J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 299 removed outlier: 3.786A pdb=" N GLN J 297 " --> pdb=" O SER J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 312 removed outlier: 3.577A pdb=" N THR J 311 " --> pdb=" O TRP J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 326 removed outlier: 3.922A pdb=" N LYS J 317 " --> pdb=" O SER J 313 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 14 removed outlier: 3.748A pdb=" N LEU K 13 " --> pdb=" O LEU K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 37 removed outlier: 3.620A pdb=" N VAL K 29 " --> pdb=" O ASN K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 57 removed outlier: 3.687A pdb=" N LYS K 55 " --> pdb=" O TYR K 51 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS K 56 " --> pdb=" O GLU K 52 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU K 57 " --> pdb=" O LEU K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 70 removed outlier: 3.696A pdb=" N ARG K 70 " --> pdb=" O GLU K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 90 Processing helix chain 'K' and resid 90 through 97 removed outlier: 4.231A pdb=" N VAL K 94 " --> pdb=" O LYS K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 113 Processing helix chain 'K' and resid 134 through 141 removed outlier: 3.525A 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 194 removed outlier: 4.519A pdb=" N LEU K 190 " --> pdb=" O GLU K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 218 removed outlier: 3.627A pdb=" N ILE K 201 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR K 217 " --> pdb=" O ALA K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 229 removed outlier: 3.632A pdb=" N ALA K 224 " --> pdb=" O SER K 220 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU K 225 " --> pdb=" O PRO K 221 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU K 226 " --> pdb=" O GLU K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 245 removed outlier: 3.589A pdb=" N ALA K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 253 Processing helix chain 'K' and resid 254 through 268 Processing helix chain 'K' and resid 268 through 285 removed outlier: 3.822A pdb=" N VAL K 272 " --> pdb=" O TYR K 268 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP K 285 " --> pdb=" O LYS K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 299 removed outlier: 3.558A pdb=" N LYS K 290 " --> pdb=" O GLY K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 312 removed outlier: 3.703A pdb=" N THR K 311 " --> pdb=" O TRP K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 326 removed outlier: 3.940A pdb=" N LYS K 317 " --> pdb=" O SER K 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 14 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 90 Processing helix chain 'L' and resid 90 through 97 removed outlier: 4.145A pdb=" N VAL L 94 " --> pdb=" O LYS L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 113 Processing helix chain 'L' and resid 134 through 141 removed outlier: 3.657A 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 194 removed outlier: 4.491A pdb=" N LEU L 190 " --> pdb=" O GLU L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 218 removed outlier: 3.599A pdb=" N ILE L 201 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR L 217 " --> pdb=" O ALA L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 229 removed outlier: 3.678A pdb=" N ALA L 224 " --> pdb=" O SER L 220 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU L 225 " --> pdb=" O PRO L 221 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU L 226 " --> pdb=" O GLU L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 245 removed outlier: 3.577A pdb=" N LEU L 240 " --> pdb=" O GLU L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 253 Processing helix chain 'L' and resid 254 through 268 Processing helix chain 'L' and resid 268 through 285 removed outlier: 3.884A pdb=" N VAL L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP L 285 " --> pdb=" O LYS L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 299 removed outlier: 3.538A pdb=" N GLU L 291 " --> pdb=" O SER L 287 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN L 297 " --> pdb=" O SER L 293 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 312 removed outlier: 3.642A pdb=" N THR L 311 " --> pdb=" O TRP L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 326 removed outlier: 3.750A pdb=" N LYS L 317 " --> pdb=" O SER L 313 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU L 325 " --> pdb=" O GLU L 321 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 8.646A pdb=" N TYR A 62 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL A 43 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 154 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET A 126 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL A 152 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA A 128 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU A 150 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 62 removed outlier: 8.794A pdb=" N TYR B 62 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL B 43 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN B 154 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N MET B 126 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL B 152 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA B 128 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU B 150 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 61 through 62 removed outlier: 8.562A pdb=" N TYR C 62 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL C 43 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN C 154 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N MET C 126 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL C 152 " --> pdb=" O MET C 126 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA C 128 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU C 150 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 5 removed outlier: 5.798A pdb=" N LEU D 150 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ALA D 128 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL D 152 " --> pdb=" O MET D 126 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N MET D 126 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN D 154 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N TYR D 62 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 43 " --> pdb=" O TYR D 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 4 through 5 removed outlier: 5.793A pdb=" N LEU E 150 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA E 128 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL E 152 " --> pdb=" O MET E 126 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET E 126 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN E 154 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N TYR E 62 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL E 43 " --> pdb=" O TYR E 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 61 through 62 removed outlier: 8.501A pdb=" N TYR F 62 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL F 43 " --> pdb=" O TYR F 62 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN F 154 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N MET F 126 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL F 152 " --> pdb=" O MET F 126 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA F 128 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LEU F 150 " --> pdb=" O ALA F 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 61 through 62 removed outlier: 8.765A pdb=" N TYR G 62 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL G 43 " --> pdb=" O TYR G 62 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN G 154 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N MET G 126 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL G 152 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA G 128 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU G 150 " --> pdb=" O ALA G 128 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 61 through 62 removed outlier: 8.568A pdb=" N TYR H 62 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL H 43 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN H 154 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N MET H 126 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL H 152 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA H 128 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU H 150 " --> pdb=" O ALA H 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 61 through 62 removed outlier: 8.716A pdb=" N TYR I 62 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL I 43 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN I 154 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N MET I 126 " --> pdb=" O VAL I 152 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL I 152 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA I 128 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU I 150 " --> pdb=" O ALA I 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 61 through 62 removed outlier: 8.703A pdb=" N TYR J 62 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL J 43 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN J 154 " --> pdb=" O THR J 124 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET J 126 " --> pdb=" O VAL J 152 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL J 152 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA J 128 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU J 150 " --> pdb=" O ALA J 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 61 through 62 removed outlier: 8.597A pdb=" N TYR K 62 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL K 43 " --> pdb=" O TYR K 62 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN K 154 " --> pdb=" O THR K 124 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET K 126 " --> pdb=" O VAL K 152 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL K 152 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA K 128 " --> pdb=" O LEU K 150 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU K 150 " --> pdb=" O ALA K 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 61 through 62 removed outlier: 8.696A pdb=" N TYR L 62 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL L 43 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY L 19 " --> pdb=" O LEU L 75 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN L 154 " --> pdb=" O THR L 124 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N MET L 126 " --> pdb=" O VAL L 152 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL L 152 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA L 128 " --> pdb=" O LEU L 150 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU L 150 " --> pdb=" O ALA L 128 " (cutoff:3.500A) 1685 hydrogen bonds defined for protein. 4857 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: 21.55 Time building geometry restraints manager: 39.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 31213 1.03 - 1.22: 12 1.22 - 1.42: 13072 1.42 - 1.61: 18296 1.61 - 1.80: 228 Bond restraints: 62821 Sorted by residual: bond pdb=" N GLY G 232 " pdb=" H GLY G 232 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" C SER G 231 " pdb=" N GLY G 232 " ideal model delta sigma weight residual 1.331 1.355 -0.025 1.46e-02 4.69e+03 2.87e+00 bond pdb=" N GLY G 232 " pdb=" CA GLY G 232 " ideal model delta sigma weight residual 1.449 1.473 -0.024 1.45e-02 4.76e+03 2.72e+00 bond pdb=" C ASP D 11 " pdb=" N PRO D 12 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.19e-02 7.06e+03 1.60e+00 bond pdb=" CA TYR D 300 " pdb=" C TYR D 300 " ideal model delta sigma weight residual 1.532 1.524 0.008 6.50e-03 2.37e+04 1.57e+00 ... (remaining 62816 not shown) Histogram of bond angle deviations from ideal: 61.36 - 77.26: 65 77.26 - 93.15: 181 93.15 - 109.05: 36144 109.05 - 124.95: 76092 124.95 - 140.84: 1504 Bond angle restraints: 113986 Sorted by residual: angle pdb=" C GLN K 30 " pdb=" N ALA K 31 " pdb=" H ALA K 31 " ideal model delta sigma weight residual 124.75 71.35 53.40 3.00e+00 1.11e-01 3.17e+02 angle pdb=" C GLY K 58 " pdb=" N PHE K 59 " pdb=" H PHE K 59 " ideal model delta sigma weight residual 124.68 71.41 53.27 3.00e+00 1.11e-01 3.15e+02 angle pdb=" CA ALA K 31 " pdb=" N ALA K 31 " pdb=" H ALA K 31 " ideal model delta sigma weight residual 114.45 61.37 53.09 3.00e+00 1.11e-01 3.13e+02 angle pdb=" CA PHE K 59 " pdb=" N PHE K 59 " pdb=" H PHE K 59 " ideal model delta sigma weight residual 114.38 61.36 53.02 3.00e+00 1.11e-01 3.12e+02 angle pdb=" C ASP J 48 " pdb=" N LYS J 49 " pdb=" H LYS J 49 " ideal model delta sigma weight residual 124.55 72.41 52.15 3.00e+00 1.11e-01 3.02e+02 ... (remaining 113981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 26685 17.97 - 35.94: 1916 35.94 - 53.92: 538 53.92 - 71.89: 70 71.89 - 89.86: 12 Dihedral angle restraints: 29221 sinusoidal: 15868 harmonic: 13353 Sorted by residual: dihedral pdb=" C ASP K 65 " pdb=" N ASP K 65 " pdb=" CA ASP K 65 " pdb=" CB ASP K 65 " ideal model delta harmonic sigma weight residual -122.60 -133.30 10.70 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" C ALA I 8 " pdb=" N ALA I 8 " pdb=" CA ALA I 8 " pdb=" CB ALA I 8 " ideal model delta harmonic sigma weight residual -122.60 -133.19 10.59 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" C LYS D 3 " pdb=" N LYS D 3 " pdb=" CA LYS D 3 " pdb=" CB LYS D 3 " ideal model delta harmonic sigma weight residual -122.60 -133.18 10.58 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 29218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.341: 4628 0.341 - 0.682: 11 0.682 - 1.023: 0 1.023 - 1.363: 4 1.363 - 1.704: 25 Chirality restraints: 4668 Sorted by residual: chirality pdb=" CG LEU C 6 " pdb=" CB LEU C 6 " pdb=" CD1 LEU C 6 " pdb=" CD2 LEU C 6 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.26e+01 chirality pdb=" CG LEU K 95 " pdb=" CB LEU K 95 " pdb=" CD1 LEU K 95 " pdb=" CD2 LEU K 95 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.16e+01 chirality pdb=" CG LEU L 13 " pdb=" CB LEU L 13 " pdb=" CD1 LEU L 13 " pdb=" CD2 LEU L 13 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.16e+01 ... (remaining 4665 not shown) Planarity restraints: 9208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 231 " 0.019 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" N GLY G 232 " -0.057 2.00e-02 2.50e+03 pdb=" CA GLY G 232 " 0.015 2.00e-02 2.50e+03 pdb=" H GLY G 232 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 11 " 0.032 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO B 12 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 12 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 12 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 11 " -0.031 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO G 12 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO G 12 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 12 " -0.026 5.00e-02 4.00e+02 ... (remaining 9205 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 2458 2.15 - 2.76: 121459 2.76 - 3.38: 167161 3.38 - 3.99: 214197 3.99 - 4.60: 349757 Nonbonded interactions: 855032 Sorted by model distance: nonbonded pdb=" H PHE K 59 " pdb=" HA PHE K 59 " model vdw 1.538 1.816 nonbonded pdb=" H LYS J 159 " pdb=" HA LYS J 159 " model vdw 1.564 1.816 nonbonded pdb=" H LYS E 159 " pdb=" HA LYS E 159 " model vdw 1.566 1.816 nonbonded pdb=" HH TYR C 229 " pdb=" OE1 GLU C 319 " model vdw 1.577 1.850 nonbonded pdb=" OE1 GLU L 60 " pdb=" H GLU L 60 " model vdw 1.593 1.850 ... (remaining 855027 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)) 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)) 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)) 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)) 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)) 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)) 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)) 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)) 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)) 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)) 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.690 Extract box with map and model: 11.190 Check model and map are aligned: 0.740 Set scattering table: 0.460 Process input model: 150.870 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 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 : 0.004 0.030 31596 Z= 0.270 Angle : 0.682 20.462 42660 Z= 0.381 Chirality : 0.126 1.704 4668 Planarity : 0.003 0.047 5424 Dihedral : 12.413 89.859 11736 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.08 % 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: -4.72 (0.10), residues: 3912 helix: -2.92 (0.08), residues: 2112 sheet: -2.28 (0.25), residues: 324 loop : -3.43 (0.13), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 198 HIS 0.004 0.001 HIS L 196 PHE 0.018 0.001 PHE G 303 TYR 0.011 0.001 TYR H 51 ARG 0.009 0.000 ARG D 69 *********************** 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 332 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 4.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.9041 (tppt) cc_final: 0.8817 (tptp) REVERT: C 99 LYS cc_start: 0.9033 (tppt) cc_final: 0.8712 (tptp) REVERT: D 99 LYS cc_start: 0.9069 (tppt) cc_final: 0.8750 (tptp) REVERT: E 96 GLN cc_start: 0.9305 (mm110) cc_final: 0.9013 (mm110) REVERT: F 99 LYS cc_start: 0.8989 (tppt) cc_final: 0.8754 (tptp) REVERT: G 99 LYS cc_start: 0.9004 (tppt) cc_final: 0.8775 (tptp) REVERT: J 96 GLN cc_start: 0.9315 (mm110) cc_final: 0.8964 (mm110) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 3.5992 time to fit residues: 1351.8660 Evaluate side-chains 232 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 3.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 196 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 300 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 7.9990 chunk 348 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 140 HIS A 278 ASN B 154 GLN B 278 ASN C 249 GLN C 278 ASN D 278 ASN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 ASN F 154 GLN F 278 ASN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN G 154 GLN G 278 ASN H 37 ASN H 278 ASN I 37 ASN I 154 GLN ** I 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 ASN J 154 GLN J 278 ASN K 278 ASN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 HIS L 278 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 31596 Z= 0.472 Angle : 0.810 17.011 42660 Z= 0.433 Chirality : 0.130 1.753 4668 Planarity : 0.004 0.055 5424 Dihedral : 4.664 23.166 4284 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.69 % Allowed : 6.24 % Favored : 93.07 % 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: -3.18 (0.12), residues: 3912 helix: -1.43 (0.10), residues: 2364 sheet: -1.17 (0.26), residues: 324 loop : -3.56 (0.13), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 198 HIS 0.012 0.003 HIS E 140 PHE 0.013 0.002 PHE D 228 TYR 0.014 0.002 TYR F 269 ARG 0.007 0.000 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 249 time to evaluate : 3.920 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: B 26 GLN cc_start: 0.8632 (mp10) cc_final: 0.8154 (mp10) REVERT: B 85 GLU cc_start: 0.8555 (mp0) cc_final: 0.8348 (mp0) REVERT: C 99 LYS cc_start: 0.9056 (tppt) cc_final: 0.8760 (tptp) REVERT: D 99 LYS cc_start: 0.9082 (tppt) cc_final: 0.8790 (tptp) REVERT: F 99 LYS cc_start: 0.9002 (tppt) cc_final: 0.8785 (tptp) REVERT: G 99 LYS cc_start: 0.9043 (tppt) cc_final: 0.8816 (tptp) REVERT: J 26 GLN cc_start: 0.8638 (mp10) cc_final: 0.8245 (mp10) REVERT: J 30 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8865 (mp10) REVERT: L 26 GLN cc_start: 0.8604 (mp10) cc_final: 0.8231 (mp10) REVERT: L 30 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8813 (mp10) outliers start: 22 outliers final: 6 residues processed: 258 average time/residue: 3.2043 time to fit residues: 954.0949 Evaluate side-chains 226 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 220 time to evaluate : 3.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain J residue 320 LYS Chi-restraints excluded: chain L residue 88 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 290 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 349 optimal weight: 0.7980 chunk 377 optimal weight: 4.9990 chunk 311 optimal weight: 0.9990 chunk 346 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 280 optimal weight: 0.5980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 ASN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN J 110 ASN ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2365 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= 0.228 Angle : 0.688 15.952 42660 Z= 0.355 Chirality : 0.129 1.721 4668 Planarity : 0.003 0.055 5424 Dihedral : 4.354 21.578 4284 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.37 % Allowed : 8.15 % Favored : 91.48 % 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: -1.97 (0.13), residues: 3912 helix: -0.48 (0.10), residues: 2352 sheet: -0.92 (0.27), residues: 324 loop : -2.93 (0.15), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 198 HIS 0.008 0.001 HIS E 140 PHE 0.009 0.001 PHE L 288 TYR 0.013 0.001 TYR H 51 ARG 0.005 0.000 ARG E 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 241 time to evaluate : 3.937 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: C 99 LYS cc_start: 0.9046 (tppt) cc_final: 0.8760 (tptp) REVERT: C 137 MET cc_start: 0.8379 (tpp) cc_final: 0.8174 (tpp) REVERT: D 99 LYS cc_start: 0.9079 (tppt) cc_final: 0.8821 (tptp) REVERT: E 9 ASN cc_start: 0.7811 (t0) cc_final: 0.7527 (t0) REVERT: F 99 LYS cc_start: 0.8990 (tppt) cc_final: 0.8784 (tptp) REVERT: J 26 GLN cc_start: 0.8664 (mp10) cc_final: 0.8326 (mp10) REVERT: L 26 GLN cc_start: 0.8669 (mp10) cc_final: 0.8385 (mp10) REVERT: L 96 GLN cc_start: 0.8352 (mp10) cc_final: 0.7962 (mp10) outliers start: 12 outliers final: 7 residues processed: 247 average time/residue: 3.1380 time to fit residues: 898.2175 Evaluate side-chains 221 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 214 time to evaluate : 3.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain K residue 30 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 0.8980 chunk 262 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 chunk 350 optimal weight: 3.9990 chunk 371 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 332 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 GLN ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 31596 Z= 0.242 Angle : 0.683 16.154 42660 Z= 0.351 Chirality : 0.129 1.713 4668 Planarity : 0.003 0.055 5424 Dihedral : 4.216 20.991 4284 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.59 % Allowed : 8.46 % Favored : 90.95 % 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: -1.18 (0.13), residues: 3912 helix: 0.19 (0.11), residues: 2292 sheet: -0.57 (0.28), residues: 324 loop : -2.57 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 198 HIS 0.009 0.002 HIS K 140 PHE 0.008 0.001 PHE J 288 TYR 0.012 0.001 TYR H 51 ARG 0.005 0.000 ARG L 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 221 time to evaluate : 3.890 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: B 270 ASP cc_start: 0.8302 (p0) cc_final: 0.8034 (p0) REVERT: C 99 LYS cc_start: 0.9051 (tppt) cc_final: 0.8778 (tptp) REVERT: D 99 LYS cc_start: 0.9088 (tppt) cc_final: 0.8830 (tptp) REVERT: E 9 ASN cc_start: 0.7854 (t0) cc_final: 0.7564 (t0) REVERT: F 99 LYS cc_start: 0.9004 (tppt) cc_final: 0.8797 (tptp) REVERT: G 96 GLN cc_start: 0.9266 (mm-40) cc_final: 0.9033 (mp10) REVERT: L 96 GLN cc_start: 0.8384 (mt0) cc_final: 0.8042 (mp10) outliers start: 19 outliers final: 7 residues processed: 231 average time/residue: 2.9815 time to fit residues: 800.7167 Evaluate side-chains 219 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 212 time to evaluate : 3.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain L residue 30 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 0.2980 chunk 210 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 276 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 316 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 333 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 110 ASN ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 ASN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 31596 Z= 0.306 Angle : 0.693 16.110 42660 Z= 0.358 Chirality : 0.129 1.718 4668 Planarity : 0.003 0.055 5424 Dihedral : 4.158 19.956 4284 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.41 % Allowed : 9.58 % Favored : 90.01 % 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: -0.96 (0.13), residues: 3912 helix: 0.26 (0.10), residues: 2376 sheet: -0.49 (0.27), residues: 360 loop : -2.48 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 198 HIS 0.008 0.002 HIS D 140 PHE 0.009 0.001 PHE J 288 TYR 0.012 0.001 TYR H 268 ARG 0.006 0.000 ARG F 274 *********************** 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 225 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 212 time to evaluate : 3.970 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: B 270 ASP cc_start: 0.8367 (p0) cc_final: 0.8113 (p0) REVERT: C 99 LYS cc_start: 0.9071 (tppt) cc_final: 0.8808 (tptp) REVERT: D 99 LYS cc_start: 0.9089 (tppt) cc_final: 0.8847 (tptp) REVERT: E 9 ASN cc_start: 0.7887 (t0) cc_final: 0.7585 (t0) REVERT: H 96 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8056 (mp10) REVERT: I 154 GLN cc_start: 0.8458 (tt0) cc_final: 0.8093 (tt0) REVERT: J 154 GLN cc_start: 0.8465 (tt0) cc_final: 0.8053 (tt0) outliers start: 13 outliers final: 6 residues processed: 220 average time/residue: 2.9066 time to fit residues: 749.6561 Evaluate side-chains 208 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 201 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain L residue 30 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 4.9990 chunk 334 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 217 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 371 optimal weight: 0.9990 chunk 308 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 31596 Z= 0.326 Angle : 0.707 16.054 42660 Z= 0.363 Chirality : 0.129 1.725 4668 Planarity : 0.003 0.055 5424 Dihedral : 4.140 19.361 4284 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.53 % Allowed : 10.08 % Favored : 89.39 % 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: -0.68 (0.13), residues: 3912 helix: 0.38 (0.11), residues: 2388 sheet: -0.37 (0.25), residues: 444 loop : -2.24 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 198 HIS 0.008 0.002 HIS B 140 PHE 0.010 0.001 PHE J 288 TYR 0.011 0.001 TYR H 51 ARG 0.007 0.000 ARG F 274 *********************** 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 217 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 200 time to evaluate : 3.997 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: B 270 ASP cc_start: 0.8424 (p0) cc_final: 0.8196 (p0) REVERT: C 99 LYS cc_start: 0.9083 (tppt) cc_final: 0.8839 (tptp) REVERT: C 319 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8620 (tt0) REVERT: E 9 ASN cc_start: 0.7931 (t0) cc_final: 0.7624 (t0) REVERT: F 30 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8876 (mp10) REVERT: I 154 GLN cc_start: 0.8521 (tt0) cc_final: 0.8132 (tt0) REVERT: J 154 GLN cc_start: 0.8545 (tt0) cc_final: 0.8174 (tt0) REVERT: K 154 GLN cc_start: 0.8517 (tt0) cc_final: 0.8134 (tt0) outliers start: 17 outliers final: 7 residues processed: 211 average time/residue: 2.8055 time to fit residues: 697.1458 Evaluate side-chains 205 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 197 time to evaluate : 4.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain L residue 30 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 210 optimal weight: 4.9990 chunk 312 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 370 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 HIS ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 140 HIS ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31596 Z= 0.222 Angle : 0.679 15.910 42660 Z= 0.346 Chirality : 0.129 1.716 4668 Planarity : 0.003 0.055 5424 Dihedral : 4.028 19.046 4284 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.41 % Allowed : 10.61 % Favored : 88.98 % 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: -0.31 (0.14), residues: 3912 helix: 0.67 (0.11), residues: 2388 sheet: 0.23 (0.28), residues: 360 loop : -2.15 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 198 HIS 0.005 0.001 HIS J 140 PHE 0.008 0.001 PHE J 288 TYR 0.014 0.001 TYR L 268 ARG 0.004 0.000 ARG F 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 207 time to evaluate : 4.037 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: C 99 LYS cc_start: 0.9081 (tppt) cc_final: 0.8863 (tptp) REVERT: C 319 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: E 9 ASN cc_start: 0.7976 (t0) cc_final: 0.7643 (t0) REVERT: E 154 GLN cc_start: 0.8617 (tt0) cc_final: 0.8300 (tt0) REVERT: F 30 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8866 (mp10) REVERT: H 30 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8283 (mp10) REVERT: I 154 GLN cc_start: 0.8508 (tt0) cc_final: 0.8106 (tt0) REVERT: J 154 GLN cc_start: 0.8512 (tt0) cc_final: 0.8132 (tt0) REVERT: K 30 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8188 (mp10) outliers start: 13 outliers final: 8 residues processed: 217 average time/residue: 2.8460 time to fit residues: 724.2908 Evaluate side-chains 208 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 197 time to evaluate : 3.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain L residue 30 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 0.0030 chunk 72 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 290 optimal weight: 5.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS I 140 HIS ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 140 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3735 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= 0.243 Angle : 0.683 15.943 42660 Z= 0.346 Chirality : 0.129 1.709 4668 Planarity : 0.003 0.055 5424 Dihedral : 3.988 18.512 4284 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.34 % Allowed : 11.05 % Favored : 88.61 % 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: -0.14 (0.14), residues: 3912 helix: 0.75 (0.11), residues: 2388 sheet: 0.14 (0.25), residues: 444 loop : -2.03 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 198 HIS 0.004 0.001 HIS D 140 PHE 0.008 0.001 PHE J 288 TYR 0.011 0.001 TYR H 51 ARG 0.004 0.000 ARG F 274 *********************** 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 209 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 198 time to evaluate : 3.961 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: C 99 LYS cc_start: 0.9111 (tppt) cc_final: 0.8881 (tptp) REVERT: C 319 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8481 (tt0) REVERT: E 9 ASN cc_start: 0.7985 (t0) cc_final: 0.7641 (t0) REVERT: E 154 GLN cc_start: 0.8642 (tt0) cc_final: 0.8309 (tt0) REVERT: F 30 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8833 (mp10) REVERT: H 30 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8270 (mp10) REVERT: H 154 GLN cc_start: 0.8702 (tt0) cc_final: 0.8402 (tt0) REVERT: I 154 GLN cc_start: 0.8520 (tt0) cc_final: 0.8116 (tt0) REVERT: J 154 GLN cc_start: 0.8528 (tt0) cc_final: 0.8144 (tt0) REVERT: K 30 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8220 (mp10) REVERT: K 154 GLN cc_start: 0.8482 (tt0) cc_final: 0.8099 (tt0) outliers start: 11 outliers final: 6 residues processed: 207 average time/residue: 2.8389 time to fit residues: 694.0055 Evaluate side-chains 206 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 197 time to evaluate : 3.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain L residue 30 GLN 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: 0.9990 chunk 323 optimal weight: 4.9990 chunk 344 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 270 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 311 optimal weight: 8.9990 chunk 326 optimal weight: 2.9990 chunk 343 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 31596 Z= 0.311 Angle : 0.701 15.951 42660 Z= 0.358 Chirality : 0.129 1.716 4668 Planarity : 0.003 0.055 5424 Dihedral : 4.014 17.988 4284 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.37 % Allowed : 11.24 % Favored : 88.39 % 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: -0.14 (0.14), residues: 3912 helix: 0.71 (0.11), residues: 2388 sheet: 0.27 (0.26), residues: 444 loop : -1.98 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 198 HIS 0.006 0.001 HIS I 140 PHE 0.010 0.001 PHE J 288 TYR 0.011 0.001 TYR H 51 ARG 0.003 0.000 ARG F 274 *********************** 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 208 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 196 time to evaluate : 3.936 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: C 30 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8748 (mp10) REVERT: C 99 LYS cc_start: 0.9114 (tppt) cc_final: 0.8910 (tptp) REVERT: C 319 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: D 30 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8748 (mp10) REVERT: E 9 ASN cc_start: 0.7988 (t0) cc_final: 0.7655 (t0) REVERT: E 154 GLN cc_start: 0.8686 (tt0) cc_final: 0.8349 (tt0) REVERT: F 30 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8788 (mp10) REVERT: H 30 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8289 (mp10) REVERT: I 154 GLN cc_start: 0.8578 (tt0) cc_final: 0.8217 (tt0) REVERT: J 154 GLN cc_start: 0.8585 (tt0) cc_final: 0.8192 (tt0) REVERT: K 30 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8227 (mp10) REVERT: K 154 GLN cc_start: 0.8536 (tt0) cc_final: 0.8154 (tt0) outliers start: 12 outliers final: 6 residues processed: 206 average time/residue: 2.7571 time to fit residues: 672.7908 Evaluate side-chains 199 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 190 time to evaluate : 3.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain L residue 30 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 4.9990 chunk 364 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 253 optimal weight: 3.9990 chunk 382 optimal weight: 1.9990 chunk 352 optimal weight: 9.9990 chunk 304 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3989 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= 0.236 Angle : 0.682 15.876 42660 Z= 0.346 Chirality : 0.129 1.722 4668 Planarity : 0.003 0.055 5424 Dihedral : 3.956 17.832 4284 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.31 % Allowed : 11.39 % Favored : 88.30 % 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: 0.10 (0.14), residues: 3912 helix: 0.89 (0.11), residues: 2388 sheet: 0.43 (0.26), residues: 444 loop : -1.89 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 198 HIS 0.003 0.001 HIS D 140 PHE 0.008 0.001 PHE J 288 TYR 0.011 0.001 TYR H 51 ARG 0.003 0.000 ARG F 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 194 time to evaluate : 4.002 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: C 30 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8734 (mp10) REVERT: C 319 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: D 30 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8747 (mp10) REVERT: E 9 ASN cc_start: 0.8012 (t0) cc_final: 0.7675 (t0) REVERT: F 30 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8776 (mp10) REVERT: H 30 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8298 (mp10) REVERT: I 154 GLN cc_start: 0.8553 (tt0) cc_final: 0.8170 (tt0) REVERT: J 30 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8203 (mp10) REVERT: J 154 GLN cc_start: 0.8572 (tt0) cc_final: 0.7982 (tt0) REVERT: K 30 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8193 (mp10) REVERT: K 154 GLN cc_start: 0.8537 (tt0) cc_final: 0.8169 (tt0) outliers start: 10 outliers final: 6 residues processed: 202 average time/residue: 2.7810 time to fit residues: 661.1649 Evaluate side-chains 200 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 4.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain L residue 30 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 0.6980 chunk 324 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 305 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 313 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.049798 restraints weight = 279635.390| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.79 r_work: 0.2650 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 31596 Z= 0.306 Angle : 0.699 15.941 42660 Z= 0.356 Chirality : 0.129 1.860 4668 Planarity : 0.003 0.054 5424 Dihedral : 3.976 17.392 4284 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.31 % Allowed : 11.42 % Favored : 88.26 % 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: 0.09 (0.14), residues: 3912 helix: 0.83 (0.11), residues: 2388 sheet: 0.53 (0.26), residues: 444 loop : -1.83 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 198 HIS 0.004 0.001 HIS D 140 PHE 0.009 0.001 PHE J 288 TYR 0.011 0.001 TYR H 51 ARG 0.003 0.000 ARG F 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13642.18 seconds wall clock time: 236 minutes 17.02 seconds (14177.02 seconds total)