Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 10:05:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq4_0750/04_2023/6kq4_0750.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq4_0750/04_2023/6kq4_0750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq4_0750/04_2023/6kq4_0750.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq4_0750/04_2023/6kq4_0750.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq4_0750/04_2023/6kq4_0750.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq4_0750/04_2023/6kq4_0750.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.417 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 24 5.21 5 S 120 5.16 5 C 20004 2.51 5 N 5076 2.21 5 O 5760 1.98 5 H 31222 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 GLU 63": "OE1" <-> "OE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 210": "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 GLU 63": "OE1" <-> "OE2" Residue "F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 63": "OE1" <-> "OE2" Residue "I TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 63": "OE1" <-> "OE2" Residue "K TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 62206 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: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5182 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "C" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5180 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "D" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "E" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "F" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "G" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "H" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "I" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "J" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "K" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5184 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "L" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5180 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.18, per 1000 atoms: 0.32 Number of scatterers: 62206 At special positions: 0 Unit cell: (143.64, 143.64, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 Mg 24 11.99 O 5760 8.00 N 5076 7.00 C 20004 6.00 H 31222 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.04 Conformation dependent library (CDL) restraints added in 4.5 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: 204 helices and 12 sheets defined 66.5% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.534A pdb=" N ARG A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 97 removed outlier: 4.780A pdb=" N ALA A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 134 through 141 removed outlier: 3.780A pdb=" N ASP A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 Processing helix chain 'A' and resid 184 through 197 removed outlier: 3.923A pdb=" N LEU A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 218 removed outlier: 3.546A pdb=" N ILE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 removed outlier: 4.218A pdb=" N LEU A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 247 through 253 removed outlier: 3.590A pdb=" N HIS A 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 268 through 285 removed outlier: 3.739A pdb=" N VAL A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.680A pdb=" N LYS A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 313 through 327 Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 48 through 57 Processing helix chain 'B' and resid 63 through 71 removed outlier: 3.534A pdb=" N ARG B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 97 removed outlier: 4.780A pdb=" N ALA B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) Proline residue: B 93 - end of helix Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 134 through 141 removed outlier: 3.779A pdb=" N ASP B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 171 Processing helix chain 'B' and resid 184 through 197 removed outlier: 3.924A pdb=" N LEU B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 218 removed outlier: 3.545A pdb=" N ILE B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 218 " --> pdb=" O VAL B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 removed outlier: 4.217A pdb=" N LEU B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 245 Processing helix chain 'B' and resid 247 through 253 removed outlier: 3.589A pdb=" N HIS B 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 268 through 285 removed outlier: 3.739A pdb=" N VAL B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.680A pdb=" N LYS B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 Processing helix chain 'B' and resid 313 through 327 Processing helix chain 'C' and resid 24 through 37 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 63 through 71 removed outlier: 3.534A pdb=" N ARG C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 97 removed outlier: 4.780A pdb=" N ALA C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 134 through 141 removed outlier: 3.780A pdb=" N ASP C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 171 Processing helix chain 'C' and resid 184 through 197 removed outlier: 3.923A pdb=" N LEU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 218 removed outlier: 3.545A pdb=" N ILE C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY C 218 " --> pdb=" O VAL C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 229 removed outlier: 4.219A pdb=" N LEU C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 245 Processing helix chain 'C' and resid 247 through 253 removed outlier: 3.589A pdb=" N HIS C 252 " --> pdb=" O GLN C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 268 Processing helix chain 'C' and resid 268 through 285 removed outlier: 3.738A pdb=" N VAL C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 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 Processing helix chain 'C' and resid 313 through 327 Processing helix chain 'D' and resid 24 through 37 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 63 through 71 removed outlier: 3.534A pdb=" N ARG D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 97 removed outlier: 4.780A pdb=" N ALA D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Proline residue: D 93 - end of helix Processing helix chain 'D' and resid 108 through 113 Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.779A pdb=" N ASP D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 184 through 197 removed outlier: 3.923A pdb=" N LEU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.546A pdb=" N ILE D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY D 218 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 229 removed outlier: 4.217A pdb=" N LEU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 245 Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.590A pdb=" N HIS D 252 " --> pdb=" O GLN D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 268 through 285 removed outlier: 3.738A pdb=" N VAL D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 removed outlier: 3.680A pdb=" N LYS D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 313 through 327 Processing helix chain 'E' and resid 24 through 37 Processing helix chain 'E' and resid 48 through 57 Processing helix chain 'E' and resid 63 through 71 removed outlier: 3.534A pdb=" N ARG E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 97 removed outlier: 4.780A pdb=" N ALA E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Proline residue: E 93 - end of helix Processing helix chain 'E' and resid 108 through 113 Processing helix chain 'E' and resid 134 through 141 removed outlier: 3.779A pdb=" N ASP E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 184 through 197 removed outlier: 3.923A pdb=" N LEU E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 218 removed outlier: 3.546A pdb=" N ILE E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY E 218 " --> pdb=" O VAL E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 229 removed outlier: 4.218A pdb=" N LEU E 226 " --> pdb=" O GLU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 245 Processing helix chain 'E' and resid 247 through 253 removed outlier: 3.589A pdb=" N HIS E 252 " --> pdb=" O GLN E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 268 through 285 removed outlier: 3.738A pdb=" N VAL E 272 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE E 275 " --> pdb=" O VAL E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 299 removed outlier: 3.680A pdb=" N LYS E 290 " --> pdb=" O GLY E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 312 Processing helix chain 'E' and resid 313 through 327 Processing helix chain 'F' and resid 24 through 37 Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.535A pdb=" N ARG F 70 " --> pdb=" O GLU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 97 removed outlier: 4.779A pdb=" N ALA F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Proline residue: F 93 - end of helix Processing helix chain 'F' and resid 108 through 113 Processing helix chain 'F' and resid 134 through 141 removed outlier: 3.779A 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: 3.924A pdb=" N LEU F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 218 removed outlier: 3.544A pdb=" N ILE F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY F 218 " --> pdb=" O VAL F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 229 removed outlier: 4.218A pdb=" N LEU F 226 " --> pdb=" O GLU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 245 Processing helix chain 'F' and resid 247 through 253 removed outlier: 3.589A pdb=" N HIS F 252 " --> pdb=" O GLN F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.738A pdb=" N VAL F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE F 275 " --> pdb=" O VAL F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 299 removed outlier: 3.681A pdb=" N LYS F 290 " --> pdb=" O GLY F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 312 Processing helix chain 'F' and resid 313 through 327 Processing helix chain 'G' and resid 24 through 37 Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 63 through 71 removed outlier: 3.534A pdb=" N ARG G 70 " --> pdb=" O GLU G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 97 removed outlier: 4.780A pdb=" N ALA G 92 " --> pdb=" O GLU G 88 " (cutoff:3.500A) Proline residue: G 93 - end of helix Processing helix chain 'G' and resid 108 through 113 Processing helix chain 'G' and resid 134 through 141 removed outlier: 3.779A pdb=" N ASP G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 171 Processing helix chain 'G' and resid 184 through 197 removed outlier: 3.924A pdb=" N LEU G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 218 removed outlier: 3.545A pdb=" N ILE G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY G 218 " --> pdb=" O VAL G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 229 removed outlier: 4.218A pdb=" N LEU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 245 Processing helix chain 'G' and resid 247 through 253 removed outlier: 3.589A pdb=" N HIS G 252 " --> pdb=" O GLN G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 268 Processing helix chain 'G' and resid 268 through 285 removed outlier: 3.738A pdb=" N VAL G 272 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE G 275 " --> pdb=" O VAL G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 299 removed outlier: 3.680A pdb=" N LYS G 290 " --> pdb=" O GLY G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 312 Processing helix chain 'G' and resid 313 through 327 Processing helix chain 'H' and resid 24 through 37 Processing helix chain 'H' and resid 48 through 57 Processing helix chain 'H' and resid 63 through 71 removed outlier: 3.535A pdb=" N ARG H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 97 removed outlier: 4.780A pdb=" N ALA H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Proline residue: H 93 - end of helix Processing helix chain 'H' and resid 108 through 113 Processing helix chain 'H' and resid 134 through 141 removed outlier: 3.779A pdb=" N ASP H 138 " --> pdb=" O GLU H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 171 Processing helix chain 'H' and resid 184 through 197 removed outlier: 3.924A pdb=" N LEU H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 218 removed outlier: 3.545A pdb=" N ILE H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY H 218 " --> pdb=" O VAL H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 229 removed outlier: 4.218A pdb=" N LEU H 226 " --> pdb=" O GLU H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 245 Processing helix chain 'H' and resid 247 through 253 removed outlier: 3.589A pdb=" N HIS H 252 " --> pdb=" O GLN H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 268 Processing helix chain 'H' and resid 268 through 285 removed outlier: 3.738A pdb=" N VAL H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE H 275 " --> pdb=" O VAL H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 299 removed outlier: 3.680A pdb=" N LYS H 290 " --> pdb=" O GLY H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 312 Processing helix chain 'H' and resid 313 through 327 Processing helix chain 'I' and resid 24 through 37 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 63 through 71 removed outlier: 3.534A pdb=" N ARG I 70 " --> pdb=" O GLU I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 97 removed outlier: 4.780A pdb=" N ALA I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) Proline residue: I 93 - end of helix Processing helix chain 'I' and resid 108 through 113 Processing helix chain 'I' and resid 134 through 141 removed outlier: 3.779A pdb=" N ASP I 138 " --> pdb=" O GLU I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 Processing helix chain 'I' and resid 184 through 197 removed outlier: 3.924A pdb=" N LEU I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 218 removed outlier: 3.546A pdb=" N ILE I 201 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY I 218 " --> pdb=" O VAL I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 229 removed outlier: 4.218A pdb=" N LEU I 226 " --> pdb=" O GLU I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 245 Processing helix chain 'I' and resid 247 through 253 removed outlier: 3.589A pdb=" N HIS I 252 " --> pdb=" O GLN I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 268 Processing helix chain 'I' and resid 268 through 285 removed outlier: 3.738A pdb=" N VAL I 272 " --> pdb=" O TYR I 268 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE I 275 " --> pdb=" O VAL I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 299 removed outlier: 3.680A pdb=" N LYS I 290 " --> pdb=" O GLY I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 312 Processing helix chain 'I' and resid 313 through 327 Processing helix chain 'J' and resid 24 through 37 Processing helix chain 'J' and resid 48 through 57 Processing helix chain 'J' and resid 63 through 71 removed outlier: 3.535A pdb=" N ARG J 70 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 97 removed outlier: 4.780A pdb=" N ALA J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) Proline residue: J 93 - end of helix Processing helix chain 'J' and resid 108 through 113 Processing helix chain 'J' and resid 134 through 141 removed outlier: 3.779A pdb=" N ASP J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 171 Processing helix chain 'J' and resid 184 through 197 removed outlier: 3.924A pdb=" N LEU J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU J 195 " --> pdb=" O ASP J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 218 removed outlier: 3.545A pdb=" N ILE J 201 " --> pdb=" O THR J 197 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY J 218 " --> pdb=" O VAL J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 229 removed outlier: 4.218A pdb=" N LEU J 226 " --> pdb=" O GLU J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 245 Processing helix chain 'J' and resid 247 through 253 removed outlier: 3.589A pdb=" N HIS J 252 " --> pdb=" O GLN J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 268 Processing helix chain 'J' and resid 268 through 285 removed outlier: 3.738A pdb=" N VAL J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE J 275 " --> pdb=" O VAL J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 299 removed outlier: 3.680A pdb=" N LYS J 290 " --> pdb=" O GLY J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 312 Processing helix chain 'J' and resid 313 through 327 Processing helix chain 'K' and resid 24 through 37 Processing helix chain 'K' and resid 48 through 57 Processing helix chain 'K' and resid 63 through 71 removed outlier: 3.535A pdb=" N ARG K 70 " --> pdb=" O GLU K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 97 removed outlier: 4.780A pdb=" N ALA K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) Proline residue: K 93 - end of helix Processing helix chain 'K' and resid 108 through 113 Processing helix chain 'K' and resid 134 through 141 removed outlier: 3.780A pdb=" N ASP K 138 " --> pdb=" O GLU K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 Processing helix chain 'K' and resid 184 through 197 removed outlier: 3.924A pdb=" N LEU K 190 " --> pdb=" O GLU K 186 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 218 removed outlier: 3.545A pdb=" N ILE K 201 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY K 218 " --> pdb=" O VAL K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 229 removed outlier: 4.218A pdb=" N LEU K 226 " --> pdb=" O GLU K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 245 Processing helix chain 'K' and resid 247 through 253 removed outlier: 3.589A pdb=" N HIS K 252 " --> pdb=" O GLN K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 268 Processing helix chain 'K' and resid 268 through 285 removed outlier: 3.738A pdb=" N VAL K 272 " --> pdb=" O TYR K 268 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE K 275 " --> pdb=" O VAL K 271 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 299 removed outlier: 3.680A pdb=" N LYS K 290 " --> pdb=" O GLY K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 312 Processing helix chain 'K' and resid 313 through 327 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 removed outlier: 3.535A pdb=" N ARG L 70 " --> pdb=" O GLU L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 97 removed outlier: 4.780A pdb=" N ALA L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) Proline residue: L 93 - end of helix Processing helix chain 'L' and resid 108 through 113 Processing helix chain 'L' and resid 134 through 141 removed outlier: 3.779A pdb=" N ASP L 138 " --> pdb=" O GLU L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 Processing helix chain 'L' and resid 184 through 197 removed outlier: 3.923A pdb=" N LEU L 190 " --> pdb=" O GLU L 186 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 218 removed outlier: 3.545A pdb=" N ILE L 201 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY L 218 " --> pdb=" O VAL L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 229 removed outlier: 4.217A pdb=" N LEU L 226 " --> pdb=" O GLU L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 245 Processing helix chain 'L' and resid 247 through 253 removed outlier: 3.588A pdb=" N HIS L 252 " --> pdb=" O GLN L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 268 Processing helix chain 'L' and resid 268 through 285 removed outlier: 3.738A pdb=" N VAL L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE L 275 " --> pdb=" O VAL L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 299 removed outlier: 3.681A pdb=" N LYS L 290 " --> pdb=" O GLY L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 312 Processing helix chain 'L' and resid 313 through 327 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.519A pdb=" N THR A 124 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA A 74 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N TYR A 62 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A 43 " --> pdb=" O TYR A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 4 through 5 removed outlier: 6.519A pdb=" N THR B 124 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA B 74 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N TYR B 62 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 43 " --> pdb=" O TYR B 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 5 removed outlier: 6.519A pdb=" N THR C 124 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA C 74 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N TYR C 62 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL C 43 " --> pdb=" O TYR C 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 5 removed outlier: 6.519A pdb=" N THR D 124 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA D 74 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N TYR D 62 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.566A 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: 6.519A pdb=" N THR E 124 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA E 74 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N TYR E 62 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL E 43 " --> pdb=" O TYR E 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 5 removed outlier: 6.519A pdb=" N THR F 124 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA F 74 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N TYR F 62 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL F 43 " --> pdb=" O TYR F 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 4 through 5 removed outlier: 6.519A pdb=" N THR G 124 " --> pdb=" O LYS G 153 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA G 74 " --> pdb=" O ASP G 104 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N TYR G 62 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL G 43 " --> pdb=" O TYR G 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 4 through 5 removed outlier: 6.520A pdb=" N THR H 124 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA H 74 " --> pdb=" O ASP H 104 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N TYR H 62 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL H 43 " --> pdb=" O TYR H 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 4 through 5 removed outlier: 6.519A pdb=" N THR I 124 " --> pdb=" O LYS I 153 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA I 74 " --> pdb=" O ASP I 104 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N TYR I 62 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL I 43 " --> pdb=" O TYR I 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 4 through 5 removed outlier: 6.519A pdb=" N THR J 124 " --> pdb=" O LYS J 153 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA J 74 " --> pdb=" O ASP J 104 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N TYR J 62 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL J 43 " --> pdb=" O TYR J 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 4 through 5 removed outlier: 6.519A pdb=" N THR K 124 " --> pdb=" O LYS K 153 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA K 74 " --> pdb=" O ASP K 104 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N TYR K 62 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL K 43 " --> pdb=" O TYR K 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 5 removed outlier: 6.519A pdb=" N THR L 124 " --> pdb=" O LYS L 153 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA L 74 " --> pdb=" O ASP L 104 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N TYR L 62 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL L 43 " --> pdb=" O TYR L 62 " (cutoff:3.500A) 1872 hydrogen bonds defined for protein. 5472 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: 21.74 Time building geometry restraints manager: 43.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 31210 1.03 - 1.22: 12 1.22 - 1.41: 13031 1.41 - 1.61: 18337 1.61 - 1.80: 228 Bond restraints: 62818 Sorted by residual: bond pdb=" CA ASP K 65 " pdb=" HA ASP K 65 " ideal model delta sigma weight residual 0.970 0.937 0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" CG GLU E 236 " pdb=" HG2 GLU E 236 " ideal model delta sigma weight residual 0.970 0.997 -0.027 2.00e-02 2.50e+03 1.81e+00 bond pdb=" CA GLY G 19 " pdb=" C GLY G 19 " ideal model delta sigma weight residual 1.520 1.511 0.009 7.30e-03 1.88e+04 1.68e+00 bond pdb=" CA GLY E 19 " pdb=" C GLY E 19 " ideal model delta sigma weight residual 1.520 1.511 0.009 7.30e-03 1.88e+04 1.61e+00 bond pdb=" CA GLY C 19 " pdb=" C GLY C 19 " ideal model delta sigma weight residual 1.520 1.511 0.009 7.30e-03 1.88e+04 1.57e+00 ... (remaining 62813 not shown) Histogram of bond angle deviations from ideal: 55.77 - 76.61: 166 76.61 - 97.45: 121 97.45 - 118.29: 85735 118.29 - 139.14: 27953 139.14 - 159.98: 3 Bond angle restraints: 113978 Sorted by residual: angle pdb=" C LYS K 55 " pdb=" N LYS K 56 " pdb=" H LYS K 56 " ideal model delta sigma weight residual 124.93 65.65 59.28 3.00e+00 1.11e-01 3.90e+02 angle pdb=" CA LYS K 56 " pdb=" N LYS K 56 " pdb=" H LYS K 56 " ideal model delta sigma weight residual 114.63 55.77 58.86 3.00e+00 1.11e-01 3.85e+02 angle pdb=" C GLN L 30 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 124.88 66.32 58.56 3.00e+00 1.11e-01 3.81e+02 angle pdb=" C GLN K 30 " pdb=" N ALA K 31 " pdb=" H ALA K 31 " ideal model delta sigma weight residual 124.88 66.38 58.50 3.00e+00 1.11e-01 3.80e+02 angle pdb=" C SER G 231 " pdb=" N GLY G 232 " pdb=" H GLY G 232 " ideal model delta sigma weight residual 124.45 65.99 58.46 3.00e+00 1.11e-01 3.80e+02 ... (remaining 113973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.58: 21926 16.58 - 33.16: 2409 33.16 - 49.74: 408 49.74 - 66.32: 76 66.32 - 82.90: 18 Dihedral angle restraints: 24837 sinusoidal: 11484 harmonic: 13353 Sorted by residual: dihedral pdb=" CA LYS C 89 " pdb=" C LYS C 89 " pdb=" N LYS C 90 " pdb=" CA LYS C 90 " ideal model delta harmonic sigma weight residual -180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA LYS F 89 " pdb=" C LYS F 89 " pdb=" N LYS F 90 " pdb=" CA LYS F 90 " ideal model delta harmonic sigma weight residual -180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA LYS H 89 " pdb=" C LYS H 89 " pdb=" N LYS H 90 " pdb=" CA LYS H 90 " ideal model delta harmonic sigma weight residual -180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 24834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3756 0.067 - 0.134: 804 0.134 - 0.201: 36 0.201 - 0.269: 36 0.269 - 0.336: 36 Chirality restraints: 4668 Sorted by residual: chirality pdb=" CB VAL I 127 " pdb=" CA VAL I 127 " pdb=" CG1 VAL I 127 " pdb=" CG2 VAL I 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CB VAL G 127 " pdb=" CA VAL G 127 " pdb=" CG1 VAL G 127 " pdb=" CG2 VAL G 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CB VAL K 127 " pdb=" CA VAL K 127 " pdb=" CG1 VAL K 127 " pdb=" CG2 VAL K 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 4665 not shown) Planarity restraints: 9208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 128 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO L 129 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO L 129 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 129 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA J 128 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO J 129 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO J 129 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO J 129 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA K 128 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO K 129 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO K 129 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO K 129 " 0.020 5.00e-02 4.00e+02 ... (remaining 9205 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 900 2.04 - 2.68: 94504 2.68 - 3.32: 176701 3.32 - 3.96: 226297 3.96 - 4.60: 368289 Nonbonded interactions: 866691 Sorted by model distance: nonbonded pdb=" H PHE K 59 " pdb=" HA PHE K 59 " model vdw 1.400 1.816 nonbonded pdb=" H GLY G 232 " pdb=" HA2 GLY G 232 " model vdw 1.401 1.816 nonbonded pdb=" O LEU F 192 " pdb=" HD1 HIS F 196 " model vdw 1.520 1.850 nonbonded pdb=" O LEU E 192 " pdb=" HD1 HIS E 196 " model vdw 1.520 1.850 nonbonded pdb=" O LEU B 192 " pdb=" HD1 HIS B 196 " model vdw 1.521 1.850 ... (remaining 866686 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401 through 402)) selection = (chain 'B' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r 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 (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 NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 401 through 40 \ 2)) selection = chain 'C' selection = (chain 'D' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401 through 402)) selection = (chain 'E' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401 through 402)) selection = (chain 'F' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1 through 402)) selection = (chain 'G' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1 through 402)) selection = (chain 'H' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401 through 402)) selection = (chain 'I' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401 through 402)) selection = (chain 'J' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401 through 402)) selection = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 329 or res \ id 401 through 402)) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.700 Extract box with map and model: 12.990 Check model and map are aligned: 0.720 Set scattering table: 0.420 Process input model: 153.390 Find NCS groups from input model: 2.810 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 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 : 0.007 0.034 31596 Z= 0.428 Angle : 0.655 4.588 42660 Z= 0.372 Chirality : 0.058 0.336 4668 Planarity : 0.004 0.036 5424 Dihedral : 13.308 74.526 11736 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.11), residues: 3912 helix: -1.89 (0.08), residues: 2436 sheet: -1.50 (0.21), residues: 504 loop : -2.72 (0.16), residues: 972 *********************** 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 567 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 555 time to evaluate : 4.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 567 average time/residue: 3.7645 time to fit residues: 2404.2131 Evaluate side-chains 303 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 295 time to evaluate : 3.951 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 4.8713 ------------------------------------------------------------------------------- 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: 5.9990 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 7.9990 chunk 348 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 154 GLN A 312 GLN B 154 GLN C 154 GLN D 26 GLN D 154 GLN F 154 GLN G 154 GLN H 26 GLN H 154 GLN I 26 GLN I 154 GLN J 96 GLN J 278 ASN K 26 GLN K 154 GLN K 278 ASN L 96 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 31596 Z= 0.304 Angle : 0.731 20.171 42660 Z= 0.384 Chirality : 0.126 1.673 4668 Planarity : 0.005 0.072 5424 Dihedral : 4.607 16.972 4284 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.13), residues: 3912 helix: -0.04 (0.10), residues: 2460 sheet: 0.23 (0.24), residues: 384 loop : -1.84 (0.17), residues: 1068 *********************** 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 346 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 310 time to evaluate : 4.041 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 outliers start: 36 outliers final: 6 residues processed: 334 average time/residue: 3.4451 time to fit residues: 1320.9381 Evaluate side-chains 275 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 269 time to evaluate : 3.964 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 1.1420 time to fit residues: 8.1176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 290 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 349 optimal weight: 2.9990 chunk 377 optimal weight: 3.9990 chunk 311 optimal weight: 7.9990 chunk 346 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 312 GLN B 26 GLN B 278 ASN B 312 GLN C 26 GLN C 154 GLN C 312 GLN D 26 GLN E 154 GLN E 312 GLN G 26 GLN H 26 GLN H 154 GLN H 312 GLN I 26 GLN I 312 GLN J 26 GLN K 26 GLN L 26 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 31596 Z= 0.392 Angle : 0.725 19.582 42660 Z= 0.382 Chirality : 0.126 1.706 4668 Planarity : 0.004 0.069 5424 Dihedral : 4.496 18.737 4284 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.13), residues: 3912 helix: 0.51 (0.10), residues: 2460 sheet: 0.63 (0.24), residues: 384 loop : -1.46 (0.18), residues: 1068 *********************** 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 323 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 276 time to evaluate : 4.113 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 outliers start: 47 outliers final: 9 residues processed: 313 average time/residue: 3.3760 time to fit residues: 1212.4260 Evaluate side-chains 271 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 262 time to evaluate : 3.975 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 2 average time/residue: 1.7225 time to fit residues: 9.1940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 chunk 350 optimal weight: 2.9990 chunk 371 optimal weight: 0.3980 chunk 183 optimal weight: 9.9990 chunk 332 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 30 GLN B 96 GLN D 26 GLN E 26 GLN F 26 GLN G 26 GLN G 30 GLN H 26 GLN I 26 GLN I 30 GLN I 96 GLN J 26 GLN J 96 GLN J 154 GLN L 26 GLN L 30 GLN L 96 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 31596 Z= 0.218 Angle : 0.678 20.238 42660 Z= 0.350 Chirality : 0.128 1.752 4668 Planarity : 0.003 0.069 5424 Dihedral : 4.207 18.586 4284 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.13), residues: 3912 helix: 1.08 (0.11), residues: 2448 sheet: 0.87 (0.25), residues: 384 loop : -1.08 (0.18), residues: 1080 *********************** 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 307 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 279 time to evaluate : 3.987 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 outliers start: 28 outliers final: 8 residues processed: 297 average time/residue: 3.4643 time to fit residues: 1180.5972 Evaluate side-chains 265 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 257 time to evaluate : 3.983 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 1.7259 time to fit residues: 9.2158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 316 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 189 optimal weight: 0.9980 chunk 333 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 154 GLN B 26 GLN B 154 GLN C 26 GLN C 30 GLN D 26 GLN D 30 GLN D 154 GLN E 26 GLN E 30 GLN E 312 GLN F 26 GLN F 30 GLN G 26 GLN H 30 GLN H 312 GLN I 26 GLN I 312 GLN J 26 GLN J 30 GLN J 154 GLN J 312 GLN K 154 GLN L 26 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.3912 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= 0.276 Angle : 0.687 20.086 42660 Z= 0.357 Chirality : 0.128 1.740 4668 Planarity : 0.003 0.072 5424 Dihedral : 4.159 18.629 4284 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.13), residues: 3912 helix: 1.24 (0.10), residues: 2448 sheet: 1.04 (0.25), residues: 384 loop : -0.92 (0.19), residues: 1080 *********************** 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 286 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 260 time to evaluate : 4.066 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 outliers start: 26 outliers final: 10 residues processed: 276 average time/residue: 3.3765 time to fit residues: 1078.9503 Evaluate side-chains 261 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 251 time to evaluate : 4.628 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 4 average time/residue: 2.0024 time to fit residues: 15.2311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 3.9990 chunk 334 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 371 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 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 96 GLN B 26 GLN B 96 GLN C 26 GLN D 96 GLN E 26 GLN E 312 GLN F 26 GLN G 26 GLN H 26 GLN H 312 GLN I 26 GLN I 30 GLN I 96 GLN I 312 GLN J 26 GLN J 96 GLN K 96 GLN L 26 GLN L 96 GLN L 154 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 31596 Z= 0.253 Angle : 0.677 20.231 42660 Z= 0.350 Chirality : 0.129 1.888 4668 Planarity : 0.003 0.041 5424 Dihedral : 4.079 18.574 4284 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.14), residues: 3912 helix: 1.40 (0.10), residues: 2448 sheet: 1.07 (0.25), residues: 384 loop : -0.77 (0.19), residues: 1080 *********************** 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 299 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 271 time to evaluate : 3.967 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 outliers start: 28 outliers final: 13 residues processed: 287 average time/residue: 3.3752 time to fit residues: 1110.6512 Evaluate side-chains 271 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 258 time to evaluate : 4.022 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 6 average time/residue: 1.7771 time to fit residues: 19.1315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 211 optimal weight: 0.8980 chunk 271 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 312 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 370 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 96 GLN C 30 GLN D 26 GLN D 30 GLN D 96 GLN E 30 GLN F 26 GLN G 30 GLN H 30 GLN J 26 GLN J 30 GLN J 96 GLN K 30 GLN L 30 GLN L 154 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 31596 Z= 0.222 Angle : 0.671 20.298 42660 Z= 0.345 Chirality : 0.130 1.819 4668 Planarity : 0.003 0.043 5424 Dihedral : 3.997 18.390 4284 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.14), residues: 3912 helix: 1.52 (0.10), residues: 2460 sheet: 1.03 (0.24), residues: 408 loop : -0.71 (0.20), residues: 1044 *********************** 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 283 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 263 time to evaluate : 3.960 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 outliers start: 20 outliers final: 16 residues processed: 274 average time/residue: 3.4035 time to fit residues: 1070.2209 Evaluate side-chains 268 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 252 time to evaluate : 4.031 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 9 average time/residue: 1.7693 time to fit residues: 25.1351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 235 optimal weight: 0.0030 chunk 252 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN F 30 GLN I 30 GLN J 26 GLN J 96 GLN K 30 GLN L 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 31596 Z= 0.227 Angle : 0.670 20.280 42660 Z= 0.345 Chirality : 0.129 1.844 4668 Planarity : 0.003 0.101 5424 Dihedral : 3.974 18.080 4284 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.14), residues: 3912 helix: 1.53 (0.10), residues: 2472 sheet: 1.05 (0.24), residues: 408 loop : -0.66 (0.20), residues: 1032 *********************** 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 276 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 257 time to evaluate : 4.165 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 outliers start: 19 outliers final: 14 residues processed: 267 average time/residue: 3.4606 time to fit residues: 1066.9556 Evaluate side-chains 267 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 253 time to evaluate : 4.260 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 8 average time/residue: 1.8922 time to fit residues: 24.1456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 5.9990 chunk 354 optimal weight: 6.9990 chunk 323 optimal weight: 0.6980 chunk 344 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 311 optimal weight: 8.9990 chunk 326 optimal weight: 0.5980 chunk 343 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN E 154 GLN G 30 GLN I 96 GLN J 30 GLN L 30 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 31596 Z= 0.172 Angle : 0.650 20.471 42660 Z= 0.331 Chirality : 0.129 1.823 4668 Planarity : 0.003 0.071 5424 Dihedral : 3.833 17.678 4284 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.14), residues: 3912 helix: 1.70 (0.10), residues: 2484 sheet: 1.05 (0.24), residues: 408 loop : -0.67 (0.20), residues: 1020 *********************** 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 290 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 273 time to evaluate : 3.996 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 outliers start: 17 outliers final: 13 residues processed: 281 average time/residue: 3.3533 time to fit residues: 1083.0456 Evaluate side-chains 256 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 243 time to evaluate : 3.975 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 9 average time/residue: 1.7121 time to fit residues: 24.3809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 6.9990 chunk 364 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 173 optimal weight: 10.0000 chunk 253 optimal weight: 3.9990 chunk 382 optimal weight: 2.9990 chunk 352 optimal weight: 3.9990 chunk 304 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 235 optimal weight: 0.6980 chunk 186 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 96 GLN B 96 GLN D 30 GLN D 96 GLN E 30 GLN F 30 GLN F 312 GLN H 30 GLN H 154 GLN I 30 GLN J 96 GLN J 154 GLN K 30 GLN K 96 GLN L 30 GLN L 96 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 31596 Z= 0.245 Angle : 0.671 20.252 42660 Z= 0.346 Chirality : 0.129 1.841 4668 Planarity : 0.004 0.079 5424 Dihedral : 3.913 17.864 4284 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.14), residues: 3912 helix: 1.67 (0.10), residues: 2460 sheet: 1.03 (0.24), residues: 408 loop : -0.66 (0.20), residues: 1044 ********************** 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 250 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 235 time to evaluate : 4.171 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 outliers start: 15 outliers final: 12 residues processed: 241 average time/residue: 3.3018 time to fit residues: 919.7842 Evaluate side-chains 238 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 226 time to evaluate : 3.988 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 10 average time/residue: 1.8390 time to fit residues: 28.4112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 4.9990 chunk 324 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 56 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: G 312 GLN I 30 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.057125 restraints weight = 197086.488| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.73 r_work: 0.2603 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 31596 Z= 0.346 Angle : 0.702 20.114 42660 Z= 0.368 Chirality : 0.130 1.860 4668 Planarity : 0.004 0.079 5424 Dihedral : 4.145 18.471 4284 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.13), residues: 3912 helix: 1.41 (0.10), residues: 2460 sheet: 0.99 (0.24), residues: 408 loop : -0.71 (0.20), residues: 1044 =============================================================================== Job complete usr+sys time: 18999.36 seconds wall clock time: 326 minutes 29.70 seconds (19589.70 seconds total)