Starting phenix.real_space_refine on Wed Feb 14 19:01:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq4_0750/02_2024/6kq4_0750.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq4_0750/02_2024/6kq4_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_0750/02_2024/6kq4_0750.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq4_0750/02_2024/6kq4_0750.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq4_0750/02_2024/6kq4_0750.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kq4_0750/02_2024/6kq4_0750.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 19.45, per 1000 atoms: 0.31 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: 37.05 Conformation dependent library (CDL) restraints added in 4.6 seconds 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... Secondary structure from input PDB file: 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: 3.57 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: 21.30 Time building geometry restraints manager: 39.20 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: 25590 16.58 - 33.16: 2746 33.16 - 49.74: 678 49.74 - 66.32: 189 66.32 - 82.90: 18 Dihedral angle restraints: 29221 sinusoidal: 15868 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 29218 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.700 Extract box with map and model: 11.710 Check model and map are aligned: 0.760 Set scattering table: 0.430 Process input model: 144.440 Find NCS groups from input model: 2.680 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:9.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.870 ------------------------------------------------------------------------------- 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 % Allowed : 0.00 % Favored : 99.63 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 198 HIS 0.002 0.001 HIS I 252 PHE 0.016 0.002 PHE I 303 TYR 0.008 0.001 TYR H 304 ARG 0.001 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 555 time to evaluate : 3.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLN cc_start: 0.8449 (tt0) cc_final: 0.7740 (tt0) REVERT: B 154 GLN cc_start: 0.8456 (tt0) cc_final: 0.7732 (tt0) REVERT: B 273 ARG cc_start: 0.8266 (ttt180) cc_final: 0.8061 (ttt90) REVERT: C 154 GLN cc_start: 0.8534 (tt0) cc_final: 0.8074 (tt0) REVERT: D 154 GLN cc_start: 0.8488 (tt0) cc_final: 0.7764 (tt0) REVERT: F 154 GLN cc_start: 0.8471 (tt0) cc_final: 0.7769 (tt0) REVERT: G 154 GLN cc_start: 0.8555 (tt0) cc_final: 0.7947 (tt0) REVERT: H 154 GLN cc_start: 0.8348 (tt0) cc_final: 0.7882 (tt0) REVERT: I 154 GLN cc_start: 0.8468 (tt0) cc_final: 0.7776 (tt0) REVERT: K 154 GLN cc_start: 0.8491 (tt0) cc_final: 0.7766 (tt0) outliers start: 12 outliers final: 8 residues processed: 567 average time/residue: 3.7454 time to fit residues: 2391.3888 Evaluate side-chains 310 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 302 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 53 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.0470 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 0.9990 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: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN D 26 GLN H 26 GLN I 26 GLN J 96 GLN J 278 ASN K 26 GLN L 96 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31596 Z= 0.221 Angle : 0.712 20.476 42660 Z= 0.371 Chirality : 0.125 1.674 4668 Planarity : 0.005 0.073 5424 Dihedral : 4.557 16.753 4300 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.84 % Allowed : 8.02 % Favored : 91.14 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 3912 helix: 0.05 (0.10), residues: 2460 sheet: -0.94 (0.21), residues: 504 loop : -1.62 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 198 HIS 0.003 0.001 HIS F 196 PHE 0.012 0.002 PHE G 303 TYR 0.010 0.001 TYR F 217 ARG 0.013 0.001 ARG G 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 332 time to evaluate : 3.802 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: A 3 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8596 (ptpp) REVERT: A 154 GLN cc_start: 0.8525 (tt0) cc_final: 0.7851 (tt0) REVERT: B 154 GLN cc_start: 0.8511 (tt0) cc_final: 0.7835 (tt0) REVERT: C 154 GLN cc_start: 0.8575 (tt0) cc_final: 0.8102 (tt0) REVERT: D 3 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8526 (mtpp) REVERT: D 154 GLN cc_start: 0.8552 (tt0) cc_final: 0.7885 (tt0) REVERT: E 3 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8538 (mtpp) REVERT: F 154 GLN cc_start: 0.8545 (tt0) cc_final: 0.7873 (tt0) REVERT: F 216 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: F 243 GLU cc_start: 0.7801 (tp30) cc_final: 0.7566 (tp30) REVERT: G 154 GLN cc_start: 0.8602 (tt0) cc_final: 0.7985 (tt0) REVERT: H 154 GLN cc_start: 0.8466 (tt0) cc_final: 0.7982 (tt0) REVERT: I 3 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8550 (mtpp) REVERT: I 154 GLN cc_start: 0.8516 (tt0) cc_final: 0.7845 (tt0) REVERT: J 26 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8461 (mm110) REVERT: K 154 GLN cc_start: 0.8535 (tt0) cc_final: 0.7865 (tt0) outliers start: 27 outliers final: 7 residues processed: 347 average time/residue: 3.4792 time to fit residues: 1372.9835 Evaluate side-chains 304 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 292 time to evaluate : 4.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain K residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 290 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 349 optimal weight: 3.9990 chunk 377 optimal weight: 4.9990 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: 4.3990 ------------------------------------------------------------------------------- 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 278 ASN B 312 GLN C 26 GLN C 312 GLN D 26 GLN E 26 GLN E 312 GLN F 312 GLN H 26 GLN H 312 GLN I 312 GLN K 26 GLN K 96 GLN K 278 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 31596 Z= 0.411 Angle : 0.739 19.370 42660 Z= 0.392 Chirality : 0.126 1.711 4668 Planarity : 0.004 0.072 5424 Dihedral : 4.527 18.837 4284 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.72 % Allowed : 8.58 % Favored : 89.70 % 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: 0.46 (0.10), residues: 2472 sheet: 0.66 (0.24), residues: 384 loop : -1.36 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 284 HIS 0.010 0.002 HIS C 196 PHE 0.017 0.003 PHE K 303 TYR 0.011 0.001 TYR C 217 ARG 0.006 0.001 ARG H 28 *********************** 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 356 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 301 time to evaluate : 3.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8792 (mtpp) REVERT: A 154 GLN cc_start: 0.8731 (tt0) cc_final: 0.8248 (tt0) REVERT: B 154 GLN cc_start: 0.8728 (tt0) cc_final: 0.8245 (tt0) REVERT: C 3 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8751 (mtpp) REVERT: C 154 GLN cc_start: 0.8743 (tt0) cc_final: 0.8255 (tt0) REVERT: D 3 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8783 (mtpp) REVERT: D 154 GLN cc_start: 0.8739 (tt0) cc_final: 0.8248 (tt0) REVERT: D 308 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: E 3 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8806 (mtpp) REVERT: E 26 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8638 (mm110) REVERT: E 154 GLN cc_start: 0.8771 (tt0) cc_final: 0.8324 (tt0) REVERT: E 215 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8542 (mttt) REVERT: F 26 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8490 (mm110) REVERT: F 154 GLN cc_start: 0.8733 (tt0) cc_final: 0.8251 (tt0) REVERT: F 216 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: F 321 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: G 3 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8739 (mtpp) REVERT: G 26 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8532 (mm110) REVERT: G 154 GLN cc_start: 0.8734 (tt0) cc_final: 0.8260 (tt0) REVERT: G 216 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: H 3 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8748 (mtpp) REVERT: H 154 GLN cc_start: 0.8736 (tt0) cc_final: 0.8265 (tt0) REVERT: H 216 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: I 3 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8786 (mtpp) REVERT: I 154 GLN cc_start: 0.8736 (tt0) cc_final: 0.8249 (tt0) REVERT: J 154 GLN cc_start: 0.8628 (tt0) cc_final: 0.8082 (tt0) REVERT: K 3 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8737 (mtpp) REVERT: K 154 GLN cc_start: 0.8739 (tt0) cc_final: 0.8246 (tt0) REVERT: L 26 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8426 (mm110) REVERT: L 154 GLN cc_start: 0.8699 (tt0) cc_final: 0.8150 (tt0) REVERT: L 321 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7542 (mp0) outliers start: 55 outliers final: 11 residues processed: 341 average time/residue: 3.3421 time to fit residues: 1303.4422 Evaluate side-chains 303 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 278 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain C residue 3 LYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain G residue 3 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain L residue 321 GLU 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: 6.9990 chunk 181 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 350 optimal weight: 1.9990 chunk 371 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 332 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN B 26 GLN C 30 GLN D 26 GLN D 30 GLN D 96 GLN E 30 GLN H 26 GLN H 30 GLN I 26 GLN J 26 GLN J 96 GLN K 30 GLN L 96 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 31596 Z= 0.239 Angle : 0.684 20.175 42660 Z= 0.355 Chirality : 0.129 1.851 4668 Planarity : 0.003 0.044 5424 Dihedral : 4.245 18.466 4284 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.25 % Allowed : 9.24 % Favored : 89.51 % 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: 0.66 (0.13), residues: 3912 helix: 1.02 (0.11), residues: 2448 sheet: 0.83 (0.24), residues: 384 loop : -0.92 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 198 HIS 0.005 0.001 HIS C 196 PHE 0.012 0.002 PHE K 303 TYR 0.010 0.001 TYR I 217 ARG 0.007 0.000 ARG G 28 *********************** 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 319 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 279 time to evaluate : 4.111 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: A 3 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8764 (mtpp) REVERT: A 154 GLN cc_start: 0.8693 (tt0) cc_final: 0.8189 (tt0) REVERT: B 154 GLN cc_start: 0.8643 (tt0) cc_final: 0.8164 (tt0) REVERT: C 3 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8744 (mtpp) REVERT: C 154 GLN cc_start: 0.8678 (tt0) cc_final: 0.8189 (tt0) REVERT: D 3 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8777 (mtpp) REVERT: D 154 GLN cc_start: 0.8656 (tt0) cc_final: 0.8164 (tt0) REVERT: E 3 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8750 (mtpp) REVERT: E 154 GLN cc_start: 0.8655 (tt0) cc_final: 0.8132 (tt0) REVERT: F 26 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8517 (mm110) REVERT: F 131 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6665 (mmp) REVERT: F 154 GLN cc_start: 0.8657 (tt0) cc_final: 0.8174 (tt0) REVERT: F 216 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: F 321 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: G 3 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8736 (mtpp) REVERT: G 26 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8534 (mm110) REVERT: G 154 GLN cc_start: 0.8675 (tt0) cc_final: 0.8195 (tt0) REVERT: G 216 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: H 3 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8745 (mtpp) REVERT: H 154 GLN cc_start: 0.8651 (tt0) cc_final: 0.8187 (tt0) REVERT: H 216 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: I 3 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8751 (mtpp) REVERT: I 154 GLN cc_start: 0.8660 (tt0) cc_final: 0.8181 (tt0) REVERT: J 154 GLN cc_start: 0.8610 (tt0) cc_final: 0.8081 (tt0) REVERT: K 3 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8763 (mtpp) REVERT: K 154 GLN cc_start: 0.8659 (tt0) cc_final: 0.8169 (tt0) REVERT: L 26 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8461 (mm110) REVERT: L 216 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7751 (mp0) outliers start: 40 outliers final: 5 residues processed: 306 average time/residue: 3.3948 time to fit residues: 1193.6363 Evaluate side-chains 286 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 267 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain C residue 3 LYS Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain G residue 3 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain L residue 216 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 316 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 333 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 96 GLN A 312 GLN B 26 GLN B 30 GLN C 26 GLN D 26 GLN E 26 GLN E 312 GLN H 26 GLN H 312 GLN I 26 GLN I 312 GLN J 26 GLN J 30 GLN J 312 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 31596 Z= 0.277 Angle : 0.685 20.046 42660 Z= 0.357 Chirality : 0.129 1.831 4668 Planarity : 0.003 0.087 5424 Dihedral : 4.158 18.755 4284 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.12 % Allowed : 10.30 % Favored : 88.58 % 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: 0.94 (0.14), residues: 3912 helix: 1.21 (0.10), residues: 2460 sheet: 0.93 (0.24), residues: 408 loop : -0.80 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 198 HIS 0.007 0.002 HIS L 196 PHE 0.013 0.002 PHE D 288 TYR 0.009 0.001 TYR L 109 ARG 0.012 0.000 ARG A 28 *********************** 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 322 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 286 time to evaluate : 3.784 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: A 3 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8774 (mtpp) REVERT: A 154 GLN cc_start: 0.8732 (tt0) cc_final: 0.8247 (tt0) REVERT: A 216 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: B 154 GLN cc_start: 0.8696 (tt0) cc_final: 0.8214 (tt0) REVERT: C 3 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8772 (mtpp) REVERT: C 154 GLN cc_start: 0.8714 (tt0) cc_final: 0.8234 (tt0) REVERT: C 216 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: D 3 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8752 (mtpp) REVERT: D 154 GLN cc_start: 0.8700 (tt0) cc_final: 0.8218 (tt0) REVERT: E 3 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8747 (mtpp) REVERT: E 96 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8059 (mp10) REVERT: E 154 GLN cc_start: 0.8668 (tt0) cc_final: 0.8127 (tt0) REVERT: F 26 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8551 (mm110) REVERT: F 131 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6972 (mmp) REVERT: F 154 GLN cc_start: 0.8698 (tt0) cc_final: 0.8211 (tt0) REVERT: F 216 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: G 3 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8751 (mtpp) REVERT: G 26 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8516 (mm110) REVERT: G 154 GLN cc_start: 0.8713 (tt0) cc_final: 0.8240 (tt0) REVERT: G 216 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: H 3 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8772 (mtpp) REVERT: H 154 GLN cc_start: 0.8724 (tt0) cc_final: 0.8261 (tt0) REVERT: H 216 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: I 3 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8740 (mtpp) REVERT: I 154 GLN cc_start: 0.8723 (tt0) cc_final: 0.8244 (tt0) REVERT: K 3 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8745 (mtpp) REVERT: K 154 GLN cc_start: 0.8700 (tt0) cc_final: 0.8204 (tt0) REVERT: L 26 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8525 (mm110) REVERT: L 154 GLN cc_start: 0.8796 (tt0) cc_final: 0.8360 (tt0) REVERT: L 216 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7770 (mp0) outliers start: 36 outliers final: 10 residues processed: 308 average time/residue: 3.4490 time to fit residues: 1211.5219 Evaluate side-chains 298 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 273 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain C residue 3 LYS Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain G residue 3 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain L residue 216 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 0.0170 chunk 334 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 0.9990 chunk 308 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 30 GLN A 96 GLN B 26 GLN C 30 GLN D 26 GLN D 30 GLN D 96 GLN E 26 GLN E 30 GLN G 30 GLN G 96 GLN H 30 GLN I 26 GLN I 30 GLN I 96 GLN J 26 GLN J 96 GLN K 30 GLN L 96 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.4134 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= 0.201 Angle : 0.664 20.329 42660 Z= 0.342 Chirality : 0.129 1.825 4668 Planarity : 0.003 0.036 5424 Dihedral : 3.998 18.390 4284 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.81 % Allowed : 10.74 % Favored : 88.45 % 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: 1.23 (0.14), residues: 3912 helix: 1.47 (0.11), residues: 2460 sheet: 0.99 (0.24), residues: 408 loop : -0.73 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 198 HIS 0.004 0.001 HIS L 196 PHE 0.011 0.002 PHE K 288 TYR 0.008 0.001 TYR L 109 ARG 0.007 0.000 ARG A 28 *********************** 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 309 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 283 time to evaluate : 3.712 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: A 3 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8759 (mtpp) REVERT: A 154 GLN cc_start: 0.8700 (tt0) cc_final: 0.8214 (tt0) REVERT: A 216 GLU cc_start: 0.8238 (mp0) cc_final: 0.7832 (mp0) REVERT: B 154 GLN cc_start: 0.8669 (tt0) cc_final: 0.8187 (tt0) REVERT: B 274 ARG cc_start: 0.8140 (tpp80) cc_final: 0.7837 (mtm-85) REVERT: C 154 GLN cc_start: 0.8689 (tt0) cc_final: 0.8209 (tt0) REVERT: C 216 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: C 274 ARG cc_start: 0.8185 (tpp80) cc_final: 0.7896 (mtm-85) REVERT: D 3 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8743 (mtpp) REVERT: D 154 GLN cc_start: 0.8680 (tt0) cc_final: 0.8184 (tt0) REVERT: E 3 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8746 (mtpp) REVERT: F 26 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8571 (mm110) REVERT: F 131 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6860 (mmp) REVERT: F 154 GLN cc_start: 0.8679 (tt0) cc_final: 0.8195 (tt0) REVERT: F 216 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: F 274 ARG cc_start: 0.8140 (tpp80) cc_final: 0.7853 (mtm-85) REVERT: G 3 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8736 (mtpp) REVERT: G 26 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8590 (mm110) REVERT: G 131 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6973 (mmp) REVERT: G 154 GLN cc_start: 0.8682 (tt0) cc_final: 0.8195 (tt0) REVERT: G 216 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: H 154 GLN cc_start: 0.8684 (tt0) cc_final: 0.8216 (tt0) REVERT: H 216 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: I 154 GLN cc_start: 0.8683 (tt0) cc_final: 0.8199 (tt0) REVERT: J 154 GLN cc_start: 0.8744 (tt0) cc_final: 0.8242 (tt0) REVERT: K 3 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8736 (mtpp) REVERT: K 154 GLN cc_start: 0.8682 (tt0) cc_final: 0.8185 (tt0) REVERT: L 26 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8456 (mm110) REVERT: L 154 GLN cc_start: 0.8758 (tt0) cc_final: 0.8309 (tt0) REVERT: L 216 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7755 (mp0) outliers start: 26 outliers final: 11 residues processed: 298 average time/residue: 3.3764 time to fit residues: 1149.9317 Evaluate side-chains 291 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 268 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain G residue 3 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain I residue 131 MET Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain L residue 216 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 271 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 312 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 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: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 312 GLN B 26 GLN B 96 GLN C 26 GLN E 26 GLN E 312 GLN F 30 GLN G 312 GLN I 26 GLN I 312 GLN J 26 GLN J 30 GLN L 30 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 31596 Z= 0.391 Angle : 0.711 19.975 42660 Z= 0.373 Chirality : 0.130 1.843 4668 Planarity : 0.004 0.090 5424 Dihedral : 4.182 18.999 4284 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.25 % Allowed : 10.58 % Favored : 88.17 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.13), residues: 3912 helix: 1.22 (0.10), residues: 2472 sheet: 1.07 (0.25), residues: 408 loop : -0.74 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 198 HIS 0.009 0.002 HIS J 196 PHE 0.015 0.002 PHE I 288 TYR 0.009 0.001 TYR L 109 ARG 0.012 0.001 ARG D 28 *********************** 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 311 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 271 time to evaluate : 3.852 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: A 3 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8793 (mtpp) REVERT: A 154 GLN cc_start: 0.8766 (tt0) cc_final: 0.8287 (tt0) REVERT: A 216 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: B 154 GLN cc_start: 0.8761 (tt0) cc_final: 0.8290 (tt0) REVERT: B 216 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: C 3 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8796 (mtpp) REVERT: C 154 GLN cc_start: 0.8746 (tt0) cc_final: 0.8273 (tt0) REVERT: D 3 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8799 (mtpp) REVERT: D 154 GLN cc_start: 0.8757 (tt0) cc_final: 0.8276 (tt0) REVERT: E 3 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8761 (mtpp) REVERT: E 154 GLN cc_start: 0.8781 (tt0) cc_final: 0.8271 (tt0) REVERT: E 216 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: F 26 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8673 (mm110) REVERT: F 131 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7093 (mmp) REVERT: F 154 GLN cc_start: 0.8757 (tt0) cc_final: 0.8281 (tt0) REVERT: F 216 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: G 3 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8778 (mtpp) REVERT: G 26 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8684 (mm110) REVERT: G 131 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.7032 (mmp) REVERT: G 154 GLN cc_start: 0.8754 (tt0) cc_final: 0.8273 (tt0) REVERT: G 216 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: H 3 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8798 (mtpp) REVERT: H 154 GLN cc_start: 0.8758 (tt0) cc_final: 0.8295 (tt0) REVERT: H 216 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: I 3 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8804 (mtpp) REVERT: I 154 GLN cc_start: 0.8759 (tt0) cc_final: 0.8282 (tt0) REVERT: J 154 GLN cc_start: 0.8787 (tt0) cc_final: 0.8280 (tt0) REVERT: K 3 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8778 (mtpp) REVERT: K 154 GLN cc_start: 0.8761 (tt0) cc_final: 0.8277 (tt0) REVERT: L 154 GLN cc_start: 0.8795 (tt0) cc_final: 0.8334 (tt0) REVERT: L 216 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7848 (mp0) outliers start: 40 outliers final: 9 residues processed: 297 average time/residue: 3.3984 time to fit residues: 1155.9863 Evaluate side-chains 290 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 264 time to evaluate : 3.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain C residue 3 LYS Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain G residue 3 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain L residue 216 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 290 optimal weight: 6.9990 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 30 GLN A 312 GLN C 30 GLN D 96 GLN E 30 GLN E 96 GLN E 312 GLN I 30 GLN I 96 GLN I 312 GLN J 26 GLN J 96 GLN L 26 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 31596 Z= 0.258 Angle : 0.680 20.291 42660 Z= 0.352 Chirality : 0.130 1.828 4668 Planarity : 0.003 0.065 5424 Dihedral : 4.081 18.721 4284 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.09 % Allowed : 11.27 % Favored : 87.64 % 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 (0.14), residues: 3912 helix: 1.37 (0.10), residues: 2472 sheet: 1.06 (0.25), residues: 408 loop : -0.65 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 198 HIS 0.005 0.001 HIS A 196 PHE 0.012 0.002 PHE K 288 TYR 0.009 0.001 TYR L 109 ARG 0.009 0.000 ARG D 28 *********************** 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 307 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 272 time to evaluate : 3.780 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: A 3 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8799 (mtpp) REVERT: A 154 GLN cc_start: 0.8733 (tt0) cc_final: 0.8261 (tt0) REVERT: B 154 GLN cc_start: 0.8717 (tt0) cc_final: 0.8236 (tt0) REVERT: C 3 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8790 (mtpp) REVERT: C 154 GLN cc_start: 0.8723 (tt0) cc_final: 0.8249 (tt0) REVERT: C 274 ARG cc_start: 0.8179 (tpp80) cc_final: 0.7858 (mtm-85) REVERT: D 3 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8788 (mtpp) REVERT: D 154 GLN cc_start: 0.8715 (tt0) cc_final: 0.8229 (tt0) REVERT: D 216 GLU cc_start: 0.8265 (mp0) cc_final: 0.7966 (mp0) REVERT: E 3 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8786 (mtpp) REVERT: E 154 GLN cc_start: 0.8758 (tt0) cc_final: 0.8263 (tt0) REVERT: F 131 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6973 (mmp) REVERT: F 154 GLN cc_start: 0.8729 (tt0) cc_final: 0.8246 (tt0) REVERT: F 216 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: F 274 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7862 (mtm-85) REVERT: G 3 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8767 (mtpp) REVERT: G 26 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8689 (mm110) REVERT: G 131 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.7014 (mmp) REVERT: G 154 GLN cc_start: 0.8724 (tt0) cc_final: 0.8250 (tt0) REVERT: G 216 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: H 3 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8785 (mtpp) REVERT: H 154 GLN cc_start: 0.8727 (tt0) cc_final: 0.8257 (tt0) REVERT: H 216 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: I 3 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8794 (mtpp) REVERT: I 154 GLN cc_start: 0.8720 (tt0) cc_final: 0.8232 (tt0) REVERT: I 216 GLU cc_start: 0.8272 (mp0) cc_final: 0.7974 (mp0) REVERT: J 154 GLN cc_start: 0.8764 (tt0) cc_final: 0.8282 (tt0) REVERT: J 216 GLU cc_start: 0.8265 (mp0) cc_final: 0.7918 (mp0) REVERT: K 3 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8781 (mtpp) REVERT: K 154 GLN cc_start: 0.8715 (tt0) cc_final: 0.8218 (tt0) REVERT: K 216 GLU cc_start: 0.8254 (mp0) cc_final: 0.7876 (mp0) REVERT: L 154 GLN cc_start: 0.8784 (tt0) cc_final: 0.8320 (tt0) outliers start: 35 outliers final: 8 residues processed: 293 average time/residue: 3.3595 time to fit residues: 1125.8832 Evaluate side-chains 288 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 267 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 3 LYS Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain G residue 3 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 249 GLN 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: 6.9990 chunk 344 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 326 optimal weight: 0.8980 chunk 343 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN D 30 GLN F 26 GLN K 30 GLN L 30 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.4403 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= 0.209 Angle : 0.665 20.433 42660 Z= 0.342 Chirality : 0.130 1.824 4668 Planarity : 0.003 0.060 5424 Dihedral : 3.948 18.543 4284 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.59 % Allowed : 11.99 % Favored : 87.42 % 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: 1.38 (0.14), residues: 3912 helix: 1.55 (0.10), residues: 2472 sheet: 1.10 (0.25), residues: 408 loop : -0.64 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 198 HIS 0.004 0.001 HIS D 196 PHE 0.011 0.002 PHE I 288 TYR 0.008 0.001 TYR E 109 ARG 0.009 0.000 ARG D 28 *********************** 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 288 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 269 time to evaluate : 3.749 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: A 154 GLN cc_start: 0.8721 (tt0) cc_final: 0.8230 (tt0) REVERT: A 274 ARG cc_start: 0.8135 (tpp80) cc_final: 0.7868 (mtm180) REVERT: B 154 GLN cc_start: 0.8716 (tt0) cc_final: 0.8224 (tt0) REVERT: C 3 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8756 (mtpp) REVERT: C 154 GLN cc_start: 0.8708 (tt0) cc_final: 0.8220 (tt0) REVERT: C 274 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7846 (mtm-85) REVERT: D 154 GLN cc_start: 0.8709 (tt0) cc_final: 0.8217 (tt0) REVERT: D 216 GLU cc_start: 0.8265 (mp0) cc_final: 0.7953 (mp0) REVERT: D 274 ARG cc_start: 0.8148 (tpp80) cc_final: 0.7873 (mtm180) REVERT: E 154 GLN cc_start: 0.8731 (tt0) cc_final: 0.8220 (tt0) REVERT: E 274 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7931 (mtm-85) REVERT: F 131 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.7059 (mmp) REVERT: F 154 GLN cc_start: 0.8714 (tt0) cc_final: 0.8220 (tt0) REVERT: F 216 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: F 274 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7894 (mtm-85) REVERT: G 3 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8745 (mtpp) REVERT: G 131 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.7041 (mmp) REVERT: G 154 GLN cc_start: 0.8699 (tt0) cc_final: 0.8211 (tt0) REVERT: G 216 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: G 274 ARG cc_start: 0.8144 (tpp80) cc_final: 0.7914 (mtm-85) REVERT: H 3 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8773 (mtpp) REVERT: H 154 GLN cc_start: 0.8702 (tt0) cc_final: 0.8217 (tt0) REVERT: H 216 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: H 274 ARG cc_start: 0.8150 (tpp80) cc_final: 0.7879 (mtm180) REVERT: I 3 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8783 (mtpp) REVERT: I 154 GLN cc_start: 0.8711 (tt0) cc_final: 0.8213 (tt0) REVERT: I 216 GLU cc_start: 0.8256 (mp0) cc_final: 0.7945 (mp0) REVERT: I 274 ARG cc_start: 0.8149 (tpp80) cc_final: 0.7876 (mtm180) REVERT: J 154 GLN cc_start: 0.8766 (tt0) cc_final: 0.8292 (tt0) REVERT: J 216 GLU cc_start: 0.8255 (mp0) cc_final: 0.7897 (mp0) REVERT: K 3 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8648 (mtpp) REVERT: K 154 GLN cc_start: 0.8715 (tt0) cc_final: 0.8209 (tt0) REVERT: K 216 GLU cc_start: 0.8252 (mp0) cc_final: 0.7882 (mp0) REVERT: K 274 ARG cc_start: 0.8136 (tpp80) cc_final: 0.7905 (mtm-85) REVERT: L 131 MET cc_start: 0.7277 (mmm) cc_final: 0.6932 (mmp) REVERT: L 154 GLN cc_start: 0.8796 (tt0) cc_final: 0.8333 (tt0) REVERT: L 216 GLU cc_start: 0.8264 (mp0) cc_final: 0.7893 (mp0) outliers start: 19 outliers final: 4 residues processed: 281 average time/residue: 3.3725 time to fit residues: 1082.8664 Evaluate side-chains 272 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 258 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 LYS Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain G residue 3 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 249 GLN 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: 1.9990 chunk 222 optimal weight: 3.9990 chunk 173 optimal weight: 9.9990 chunk 253 optimal weight: 3.9990 chunk 382 optimal weight: 2.9990 chunk 352 optimal weight: 0.6980 chunk 304 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 235 optimal weight: 0.1980 chunk 186 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 D 96 GLN F 30 GLN G 26 GLN H 30 GLN J 26 GLN J 30 GLN J 96 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 31596 Z= 0.160 Angle : 0.647 20.607 42660 Z= 0.328 Chirality : 0.129 1.848 4668 Planarity : 0.003 0.054 5424 Dihedral : 3.753 17.829 4284 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.44 % Allowed : 12.20 % Favored : 87.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.14), residues: 3912 helix: 1.80 (0.10), residues: 2472 sheet: 1.06 (0.25), residues: 408 loop : -0.64 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 198 HIS 0.002 0.001 HIS H 196 PHE 0.011 0.001 PHE K 184 TYR 0.007 0.001 TYR G 51 ARG 0.008 0.000 ARG D 28 ********************** 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 290 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 276 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8727 (mtpp) REVERT: A 154 GLN cc_start: 0.8671 (tt0) cc_final: 0.8194 (tt0) REVERT: B 154 GLN cc_start: 0.8659 (tt0) cc_final: 0.8166 (tt0) REVERT: B 216 GLU cc_start: 0.8252 (mp0) cc_final: 0.7875 (mp0) REVERT: B 274 ARG cc_start: 0.8123 (tpp80) cc_final: 0.7844 (mtm110) REVERT: C 3 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8724 (mtpp) REVERT: C 154 GLN cc_start: 0.8667 (tt0) cc_final: 0.8168 (tt0) REVERT: C 274 ARG cc_start: 0.8150 (tpp80) cc_final: 0.7855 (mtm-85) REVERT: D 154 GLN cc_start: 0.8688 (tt0) cc_final: 0.8190 (tt0) REVERT: D 274 ARG cc_start: 0.8121 (tpp80) cc_final: 0.7902 (mtm-85) REVERT: E 154 GLN cc_start: 0.8679 (tt0) cc_final: 0.8184 (tt0) REVERT: E 274 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7912 (mtm-85) REVERT: F 131 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6943 (mmp) REVERT: F 154 GLN cc_start: 0.8675 (tt0) cc_final: 0.8181 (tt0) REVERT: F 216 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: F 274 ARG cc_start: 0.8128 (tpp80) cc_final: 0.7898 (mtm-85) REVERT: G 3 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8727 (mtpp) REVERT: G 154 GLN cc_start: 0.8677 (tt0) cc_final: 0.8178 (tt0) REVERT: G 216 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: G 274 ARG cc_start: 0.8130 (tpp80) cc_final: 0.7905 (mtm-85) REVERT: H 3 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8728 (mtpp) REVERT: H 154 GLN cc_start: 0.8670 (tt0) cc_final: 0.8181 (tt0) REVERT: H 216 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: H 274 ARG cc_start: 0.8121 (tpp80) cc_final: 0.7906 (mtm-85) REVERT: I 3 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8744 (mtpp) REVERT: I 154 GLN cc_start: 0.8655 (tt0) cc_final: 0.8155 (tt0) REVERT: I 274 ARG cc_start: 0.8124 (tpp80) cc_final: 0.7908 (mtm-85) REVERT: J 154 GLN cc_start: 0.8741 (tt0) cc_final: 0.8276 (tt0) REVERT: J 216 GLU cc_start: 0.8209 (mp0) cc_final: 0.7868 (mp0) REVERT: J 274 ARG cc_start: 0.8134 (tpp80) cc_final: 0.7850 (mtm110) REVERT: K 154 GLN cc_start: 0.8670 (tt0) cc_final: 0.8163 (tt0) REVERT: K 274 ARG cc_start: 0.8105 (tpp80) cc_final: 0.7884 (mtm-85) REVERT: L 131 MET cc_start: 0.7262 (mmm) cc_final: 0.7025 (OUTLIER) REVERT: L 154 GLN cc_start: 0.8737 (tt0) cc_final: 0.8299 (tt0) REVERT: L 216 GLU cc_start: 0.8245 (mp0) cc_final: 0.7884 (mp0) REVERT: L 274 ARG cc_start: 0.8143 (tpp80) cc_final: 0.7851 (mtm110) outliers start: 14 outliers final: 4 residues processed: 283 average time/residue: 3.4379 time to fit residues: 1114.6646 Evaluate side-chains 262 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 250 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain C residue 3 LYS Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain G residue 3 LYS Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain I residue 3 LYS 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: 0.9990 chunk 93 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 GLN F 26 GLN G 26 GLN G 30 GLN K 30 GLN L 30 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.085476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.058464 restraints weight = 194057.979| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.89 r_work: 0.2625 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.4522 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= 0.280 Angle : 0.680 20.286 42660 Z= 0.351 Chirality : 0.129 1.828 4668 Planarity : 0.003 0.095 5424 Dihedral : 3.901 18.268 4284 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.47 % Allowed : 12.58 % Favored : 86.95 % 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: 1.44 (0.14), residues: 3912 helix: 1.61 (0.10), residues: 2472 sheet: 1.10 (0.25), residues: 408 loop : -0.64 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 198 HIS 0.005 0.001 HIS H 196 PHE 0.014 0.002 PHE K 288 TYR 0.009 0.001 TYR D 300 ARG 0.014 0.001 ARG C 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19848.46 seconds wall clock time: 340 minutes 45.74 seconds (20445.74 seconds total)