Starting phenix.real_space_refine on Fri Apr 12 18:10:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbd_17585/04_2024/8pbd_17585_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbd_17585/04_2024/8pbd_17585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbd_17585/04_2024/8pbd_17585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbd_17585/04_2024/8pbd_17585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbd_17585/04_2024/8pbd_17585_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbd_17585/04_2024/8pbd_17585_updated.pdb" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.072 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 Ca 20 9.91 5 P 84 5.49 5 S 139 5.16 5 C 16254 2.51 5 N 4665 2.21 5 O 5204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26366 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "E" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "F" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "G" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "H" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "I" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "J" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "K" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 3, 'TRANS': 12} Chain: "L" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 3, 'TRANS': 12} Chain: "M" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 3, 'TRANS': 12} Chain: "N" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 3, 'TRANS': 12} Chain: "O" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 3, 'TRANS': 12} Chain: "P" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 3, 'TRANS': 12} Chain: "Q" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 3, 'TRANS': 12} Chain: "R" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 3, 'TRANS': 12} Chain: "S" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 3, 'TRANS': 12} Chain: "T" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 585 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "U" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 522 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.24, per 1000 atoms: 0.54 Number of scatterers: 26366 At special positions: 0 Unit cell: (123.88, 121.272, 220.376, 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) Ca 20 19.99 S 139 16.00 P 84 15.00 O 5204 8.00 N 4665 7.00 C 16254 6.00 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: 10.40 Conformation dependent library (CDL) restraints added in 4.6 seconds 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 150 helices and 30 sheets defined 42.4% alpha, 13.2% beta 20 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 12.21 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.796A pdb=" N GLN A 30 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 removed outlier: 3.848A pdb=" N ALA A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 80 Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 107 through 113 removed outlier: 3.589A pdb=" N LEU A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 145 removed outlier: 5.229A pdb=" N GLN A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 168 through 178 removed outlier: 3.550A pdb=" N VAL A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.774A pdb=" N ASP A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 213 removed outlier: 3.935A pdb=" N LEU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 238 through 258 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.530A pdb=" N ALA A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 31 removed outlier: 3.795A pdb=" N GLN B 30 " --> pdb=" O ARG B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 44 removed outlier: 3.848A pdb=" N ALA B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 68 through 80 Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 107 through 113 removed outlier: 3.590A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 145 removed outlier: 5.228A pdb=" N GLN B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.550A pdb=" N VAL B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.774A pdb=" N ASP B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 213 removed outlier: 3.935A pdb=" N LEU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 231 No H-bonds generated for 'chain 'B' and resid 228 through 231' Processing helix chain 'B' and resid 238 through 258 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.530A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 31 removed outlier: 3.796A pdb=" N GLN C 30 " --> pdb=" O ARG C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.847A pdb=" N ALA C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 68 through 80 Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 107 through 113 removed outlier: 3.590A pdb=" N LEU C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 145 removed outlier: 5.229A pdb=" N GLN C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.550A pdb=" N VAL C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 removed outlier: 3.774A pdb=" N ASP C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 213 removed outlier: 3.935A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 231 No H-bonds generated for 'chain 'C' and resid 228 through 231' Processing helix chain 'C' and resid 238 through 258 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.531A pdb=" N ALA C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 31 removed outlier: 3.795A pdb=" N GLN D 30 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 removed outlier: 3.848A pdb=" N ALA D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 53 Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 107 through 113 removed outlier: 3.590A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 145 removed outlier: 5.228A pdb=" N GLN D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 168 through 178 removed outlier: 3.550A pdb=" N VAL D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 removed outlier: 3.774A pdb=" N ASP D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 213 removed outlier: 3.935A pdb=" N LEU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA D 209 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 231 No H-bonds generated for 'chain 'D' and resid 228 through 231' Processing helix chain 'D' and resid 238 through 258 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.529A pdb=" N ALA D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 31 removed outlier: 3.796A pdb=" N GLN E 30 " --> pdb=" O ARG E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 44 removed outlier: 3.848A pdb=" N ALA E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 53 Processing helix chain 'E' and resid 57 through 61 Processing helix chain 'E' and resid 68 through 80 Processing helix chain 'E' and resid 89 through 97 Processing helix chain 'E' and resid 107 through 113 removed outlier: 3.589A pdb=" N LEU E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 145 removed outlier: 5.228A pdb=" N GLN E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 168 through 178 removed outlier: 3.550A pdb=" N VAL E 174 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 187 removed outlier: 3.773A pdb=" N ASP E 187 " --> pdb=" O SER E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 213 removed outlier: 3.935A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA E 209 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 231 No H-bonds generated for 'chain 'E' and resid 228 through 231' Processing helix chain 'E' and resid 238 through 258 Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.530A pdb=" N ALA E 295 " --> pdb=" O ILE E 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 31 removed outlier: 3.795A pdb=" N GLN F 30 " --> pdb=" O ARG F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 44 removed outlier: 3.848A pdb=" N ALA F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 57 through 61 Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'F' and resid 89 through 97 Processing helix chain 'F' and resid 107 through 113 removed outlier: 3.589A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 145 removed outlier: 5.228A pdb=" N GLN F 145 " --> pdb=" O ALA F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 168 through 178 removed outlier: 3.549A pdb=" N VAL F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 187 removed outlier: 3.774A pdb=" N ASP F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 213 removed outlier: 3.936A pdb=" N LEU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA F 209 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 231 No H-bonds generated for 'chain 'F' and resid 228 through 231' Processing helix chain 'F' and resid 238 through 258 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.531A pdb=" N ALA F 295 " --> pdb=" O ILE F 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 31 removed outlier: 3.795A pdb=" N GLN G 30 " --> pdb=" O ARG G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 44 removed outlier: 3.848A pdb=" N ALA G 44 " --> pdb=" O LYS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'G' and resid 57 through 61 Processing helix chain 'G' and resid 68 through 80 Processing helix chain 'G' and resid 89 through 97 Processing helix chain 'G' and resid 107 through 113 removed outlier: 3.590A pdb=" N LEU G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 145 removed outlier: 5.229A pdb=" N GLN G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 150 No H-bonds generated for 'chain 'G' and resid 148 through 150' Processing helix chain 'G' and resid 168 through 178 removed outlier: 3.550A pdb=" N VAL G 174 " --> pdb=" O ARG G 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 187 removed outlier: 3.774A pdb=" N ASP G 187 " --> pdb=" O SER G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 213 removed outlier: 3.936A pdb=" N LEU G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 209 " --> pdb=" O TYR G 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 231 No H-bonds generated for 'chain 'G' and resid 228 through 231' Processing helix chain 'G' and resid 238 through 258 Processing helix chain 'G' and resid 289 through 295 removed outlier: 3.531A pdb=" N ALA G 295 " --> pdb=" O ILE G 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 31 removed outlier: 3.796A pdb=" N GLN H 30 " --> pdb=" O ARG H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 44 removed outlier: 3.848A pdb=" N ALA H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 53 Processing helix chain 'H' and resid 57 through 61 Processing helix chain 'H' and resid 68 through 80 Processing helix chain 'H' and resid 89 through 97 Processing helix chain 'H' and resid 107 through 113 removed outlier: 3.590A pdb=" N LEU H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 145 removed outlier: 5.229A pdb=" N GLN H 145 " --> pdb=" O ALA H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 150 No H-bonds generated for 'chain 'H' and resid 148 through 150' Processing helix chain 'H' and resid 168 through 178 removed outlier: 3.551A pdb=" N VAL H 174 " --> pdb=" O ARG H 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 187 removed outlier: 3.773A pdb=" N ASP H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 213 removed outlier: 3.935A pdb=" N LEU H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA H 209 " --> pdb=" O TYR H 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL H 212 " --> pdb=" O SER H 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU H 213 " --> pdb=" O ALA H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 231 No H-bonds generated for 'chain 'H' and resid 228 through 231' Processing helix chain 'H' and resid 238 through 258 Processing helix chain 'H' and resid 289 through 295 removed outlier: 3.530A pdb=" N ALA H 295 " --> pdb=" O ILE H 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 31 removed outlier: 3.796A pdb=" N GLN I 30 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 44 removed outlier: 3.847A pdb=" N ALA I 44 " --> pdb=" O LYS I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 53 Processing helix chain 'I' and resid 57 through 61 Processing helix chain 'I' and resid 68 through 80 Processing helix chain 'I' and resid 89 through 97 Processing helix chain 'I' and resid 107 through 113 removed outlier: 3.590A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 145 removed outlier: 5.229A pdb=" N GLN I 145 " --> pdb=" O ALA I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 150 No H-bonds generated for 'chain 'I' and resid 148 through 150' Processing helix chain 'I' and resid 168 through 178 removed outlier: 3.550A pdb=" N VAL I 174 " --> pdb=" O ARG I 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 187 removed outlier: 3.774A pdb=" N ASP I 187 " --> pdb=" O SER I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 213 removed outlier: 3.935A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA I 209 " --> pdb=" O TYR I 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU I 213 " --> pdb=" O ALA I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 231 No H-bonds generated for 'chain 'I' and resid 228 through 231' Processing helix chain 'I' and resid 238 through 258 Processing helix chain 'I' and resid 289 through 295 removed outlier: 3.530A pdb=" N ALA I 295 " --> pdb=" O ILE I 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 31 removed outlier: 3.797A pdb=" N GLN J 30 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 44 removed outlier: 3.847A pdb=" N ALA J 44 " --> pdb=" O LYS J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 57 through 61 Processing helix chain 'J' and resid 68 through 80 Processing helix chain 'J' and resid 89 through 97 Processing helix chain 'J' and resid 107 through 113 removed outlier: 3.589A pdb=" N LEU J 112 " --> pdb=" O GLU J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 145 removed outlier: 5.228A pdb=" N GLN J 145 " --> pdb=" O ALA J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 150 No H-bonds generated for 'chain 'J' and resid 148 through 150' Processing helix chain 'J' and resid 168 through 178 removed outlier: 3.550A pdb=" N VAL J 174 " --> pdb=" O ARG J 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG J 177 " --> pdb=" O ALA J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 187 removed outlier: 3.774A pdb=" N ASP J 187 " --> pdb=" O SER J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 213 removed outlier: 3.935A pdb=" N LEU J 204 " --> pdb=" O GLN J 200 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR J 205 " --> pdb=" O THR J 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA J 209 " --> pdb=" O TYR J 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL J 212 " --> pdb=" O SER J 208 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU J 213 " --> pdb=" O ALA J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 231 No H-bonds generated for 'chain 'J' and resid 228 through 231' Processing helix chain 'J' and resid 238 through 258 Processing helix chain 'J' and resid 289 through 295 removed outlier: 3.530A pdb=" N ALA J 295 " --> pdb=" O ILE J 291 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 298 through 302 removed outlier: 3.624A pdb=" N GLY A 127 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A 219 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR A 266 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL A 221 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET A 158 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP A 222 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 160 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 269 through 271 Processing sheet with id= C, first strand: chain 'A' and resid 309 through 313 Processing sheet with id= D, first strand: chain 'B' and resid 298 through 302 removed outlier: 3.624A pdb=" N GLY B 127 " --> pdb=" O ASN B 267 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 219 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR B 266 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL B 221 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET B 158 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP B 222 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 160 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 269 through 271 Processing sheet with id= F, first strand: chain 'B' and resid 309 through 313 Processing sheet with id= G, first strand: chain 'C' and resid 298 through 302 removed outlier: 3.624A pdb=" N GLY C 127 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU C 219 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR C 266 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C 221 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET C 158 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP C 222 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE C 160 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 269 through 271 Processing sheet with id= I, first strand: chain 'C' and resid 309 through 313 Processing sheet with id= J, first strand: chain 'D' and resid 298 through 302 removed outlier: 3.623A pdb=" N GLY D 127 " --> pdb=" O ASN D 267 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU D 219 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR D 266 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL D 221 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET D 158 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP D 222 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE D 160 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 269 through 271 Processing sheet with id= L, first strand: chain 'D' and resid 309 through 313 Processing sheet with id= M, first strand: chain 'E' and resid 298 through 302 removed outlier: 3.624A pdb=" N GLY E 127 " --> pdb=" O ASN E 267 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU E 219 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR E 266 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL E 221 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET E 158 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP E 222 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE E 160 " --> pdb=" O ASP E 222 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 269 through 271 Processing sheet with id= O, first strand: chain 'E' and resid 309 through 313 Processing sheet with id= P, first strand: chain 'F' and resid 298 through 302 removed outlier: 3.623A pdb=" N GLY F 127 " --> pdb=" O ASN F 267 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU F 219 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR F 266 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL F 221 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET F 158 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP F 222 " --> pdb=" O MET F 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE F 160 " --> pdb=" O ASP F 222 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 269 through 271 Processing sheet with id= R, first strand: chain 'F' and resid 309 through 313 Processing sheet with id= S, first strand: chain 'G' and resid 298 through 302 removed outlier: 3.623A pdb=" N GLY G 127 " --> pdb=" O ASN G 267 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU G 219 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR G 266 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL G 221 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET G 158 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP G 222 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE G 160 " --> pdb=" O ASP G 222 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 269 through 271 Processing sheet with id= U, first strand: chain 'G' and resid 309 through 313 Processing sheet with id= V, first strand: chain 'H' and resid 298 through 302 removed outlier: 3.623A pdb=" N GLY H 127 " --> pdb=" O ASN H 267 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU H 219 " --> pdb=" O VAL H 264 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR H 266 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL H 221 " --> pdb=" O THR H 266 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET H 158 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP H 222 " --> pdb=" O MET H 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE H 160 " --> pdb=" O ASP H 222 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 269 through 271 Processing sheet with id= X, first strand: chain 'H' and resid 309 through 313 Processing sheet with id= Y, first strand: chain 'I' and resid 298 through 302 removed outlier: 3.624A pdb=" N GLY I 127 " --> pdb=" O ASN I 267 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU I 219 " --> pdb=" O VAL I 264 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR I 266 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL I 221 " --> pdb=" O THR I 266 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET I 158 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP I 222 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE I 160 " --> pdb=" O ASP I 222 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 269 through 271 Processing sheet with id= AA, first strand: chain 'I' and resid 309 through 313 Processing sheet with id= AB, first strand: chain 'J' and resid 298 through 302 removed outlier: 3.624A pdb=" N GLY J 127 " --> pdb=" O ASN J 267 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU J 219 " --> pdb=" O VAL J 264 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR J 266 " --> pdb=" O LEU J 219 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL J 221 " --> pdb=" O THR J 266 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET J 158 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP J 222 " --> pdb=" O MET J 158 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE J 160 " --> pdb=" O ASP J 222 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 269 through 271 Processing sheet with id= AD, first strand: chain 'J' and resid 309 through 313 910 hydrogen bonds defined for protein. 2580 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 10.65 Time building geometry restraints manager: 11.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6155 1.33 - 1.45: 5382 1.45 - 1.57: 14983 1.57 - 1.69: 136 1.69 - 1.81: 219 Bond restraints: 26875 Sorted by residual: bond pdb=" CA TYR G 232 " pdb=" CB TYR G 232 " ideal model delta sigma weight residual 1.528 1.502 0.026 1.51e-02 4.39e+03 3.04e+00 bond pdb=" CA TYR F 232 " pdb=" CB TYR F 232 " ideal model delta sigma weight residual 1.528 1.502 0.026 1.51e-02 4.39e+03 3.00e+00 bond pdb=" CA TYR H 232 " pdb=" CB TYR H 232 " ideal model delta sigma weight residual 1.528 1.503 0.026 1.51e-02 4.39e+03 2.93e+00 bond pdb=" CA TYR D 232 " pdb=" CB TYR D 232 " ideal model delta sigma weight residual 1.528 1.503 0.026 1.51e-02 4.39e+03 2.92e+00 bond pdb=" CA TYR B 232 " pdb=" CB TYR B 232 " ideal model delta sigma weight residual 1.528 1.503 0.026 1.51e-02 4.39e+03 2.89e+00 ... (remaining 26870 not shown) Histogram of bond angle deviations from ideal: 98.82 - 106.94: 1154 106.94 - 115.07: 16378 115.07 - 123.19: 17905 123.19 - 131.32: 1074 131.32 - 139.44: 39 Bond angle restraints: 36550 Sorted by residual: angle pdb=" C PHE A 129 " pdb=" N ARG A 130 " pdb=" CA ARG A 130 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.97e+00 angle pdb=" C PHE J 129 " pdb=" N ARG J 130 " pdb=" CA ARG J 130 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.97e+00 angle pdb=" C PHE C 129 " pdb=" N ARG C 130 " pdb=" CA ARG C 130 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.95e+00 angle pdb=" C PHE I 129 " pdb=" N ARG I 130 " pdb=" CA ARG I 130 " ideal model delta sigma weight residual 121.54 127.53 -5.99 1.91e+00 2.74e-01 9.84e+00 angle pdb=" C PHE D 129 " pdb=" N ARG D 130 " pdb=" CA ARG D 130 " ideal model delta sigma weight residual 121.54 127.52 -5.98 1.91e+00 2.74e-01 9.81e+00 ... (remaining 36545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.81: 15674 30.81 - 61.62: 665 61.62 - 92.43: 41 92.43 - 123.24: 0 123.24 - 154.05: 1 Dihedral angle restraints: 16381 sinusoidal: 7088 harmonic: 9293 Sorted by residual: dihedral pdb=" C4' DT U 1 " pdb=" C3' DT U 1 " pdb=" O3' DT U 1 " pdb=" P DC U 2 " ideal model delta sinusoidal sigma weight residual 220.00 65.95 154.05 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA ASP H 316 " pdb=" CB ASP H 316 " pdb=" CG ASP H 316 " pdb=" OD1 ASP H 316 " ideal model delta sinusoidal sigma weight residual -30.00 -83.00 53.00 1 2.00e+01 2.50e-03 9.56e+00 dihedral pdb=" CA ASP A 316 " pdb=" CB ASP A 316 " pdb=" CG ASP A 316 " pdb=" OD1 ASP A 316 " ideal model delta sinusoidal sigma weight residual -30.00 -82.98 52.98 1 2.00e+01 2.50e-03 9.55e+00 ... (remaining 16378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2289 0.028 - 0.057: 1210 0.057 - 0.085: 413 0.085 - 0.113: 214 0.113 - 0.141: 13 Chirality restraints: 4139 Sorted by residual: chirality pdb=" C3' DG T 2 " pdb=" C4' DG T 2 " pdb=" O3' DG T 2 " pdb=" C2' DG T 2 " both_signs ideal model delta sigma weight residual False -2.66 -2.52 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA VAL L3290 " pdb=" N VAL L3290 " pdb=" C VAL L3290 " pdb=" CB VAL L3290 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA VAL M3290 " pdb=" N VAL M3290 " pdb=" C VAL M3290 " pdb=" CB VAL M3290 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 4136 not shown) Planarity restraints: 4521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA T 18 " 0.015 2.00e-02 2.50e+03 6.92e-03 1.32e+00 pdb=" N9 DA T 18 " -0.016 2.00e-02 2.50e+03 pdb=" C8 DA T 18 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA T 18 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA T 18 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA T 18 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA T 18 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DA T 18 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA T 18 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA T 18 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA T 18 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA T 15 " 0.014 2.00e-02 2.50e+03 6.32e-03 1.10e+00 pdb=" N9 DA T 15 " -0.014 2.00e-02 2.50e+03 pdb=" C8 DA T 15 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA T 15 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA T 15 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA T 15 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA T 15 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DA T 15 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA T 15 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA T 15 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA T 15 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 167 " -0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO E 168 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO E 168 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 168 " -0.014 5.00e-02 4.00e+02 ... (remaining 4518 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 942 2.70 - 3.25: 26836 3.25 - 3.80: 41871 3.80 - 4.35: 59509 4.35 - 4.90: 95785 Nonbonded interactions: 224943 Sorted by model distance: nonbonded pdb=" OG1 THR G 134 " pdb="CA CA G 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR I 134 " pdb="CA CA I 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR H 134 " pdb="CA CA H 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR D 134 " pdb="CA CA D 401 " model vdw 2.152 2.510 nonbonded pdb=" OG1 THR C 134 " pdb="CA CA C 401 " model vdw 2.152 2.510 ... (remaining 224938 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 21 through 339 or resid 401 through 402)) selection = (chain 'B' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'C' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'D' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'E' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'F' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'G' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'H' and (resid 21 through 339 or resid 400 through 401)) selection = (chain 'I' and (resid 21 through 339 or resid 400 through 401)) selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.500 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 79.170 Find NCS groups from input model: 2.490 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 0.041 26875 Z= 0.479 Angle : 0.522 6.030 36550 Z= 0.283 Chirality : 0.041 0.141 4139 Planarity : 0.003 0.025 4521 Dihedral : 15.391 154.054 10413 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.23 % Favored : 93.46 % Rotamer: Outliers : 1.92 % Allowed : 6.14 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.11), residues: 3196 helix: -2.99 (0.09), residues: 1360 sheet: -2.18 (0.23), residues: 480 loop : -2.77 (0.12), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 294 PHE 0.009 0.001 PHE G 126 TYR 0.009 0.001 TYR B 301 ARG 0.004 0.001 ARG I 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 874 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7490 (mtpp) cc_final: 0.6507 (mtpt) REVERT: A 68 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6575 (tm-30) REVERT: A 94 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8224 (mt0) REVERT: A 176 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6973 (mm-30) REVERT: A 202 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8085 (tt0) REVERT: A 247 ARG cc_start: 0.8231 (mtp-110) cc_final: 0.7992 (mmm-85) REVERT: A 303 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7607 (mtm180) REVERT: A 329 ILE cc_start: 0.8060 (mt) cc_final: 0.7774 (mt) REVERT: B 26 SER cc_start: 0.7862 (p) cc_final: 0.7366 (p) REVERT: B 33 ILE cc_start: 0.8471 (mm) cc_final: 0.8228 (mm) REVERT: B 42 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7296 (mt-10) REVERT: B 43 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7352 (pp20) REVERT: B 94 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8078 (mm-40) REVERT: B 95 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7741 (ttt-90) REVERT: B 206 GLN cc_start: 0.8094 (mt0) cc_final: 0.7863 (mt0) REVERT: B 232 TYR cc_start: 0.9070 (m-80) cc_final: 0.8851 (m-80) REVERT: C 82 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8796 (p) REVERT: C 94 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7421 (tp40) REVERT: C 95 ARG cc_start: 0.8339 (ttp80) cc_final: 0.7782 (ttp-170) REVERT: C 107 LYS cc_start: 0.8249 (mmtm) cc_final: 0.7905 (ptpp) REVERT: C 154 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7230 (mt-10) REVERT: C 202 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7717 (mt0) REVERT: C 216 TYR cc_start: 0.8968 (m-80) cc_final: 0.8728 (m-80) REVERT: C 232 TYR cc_start: 0.9196 (m-80) cc_final: 0.8853 (m-80) REVERT: C 251 MET cc_start: 0.8319 (ttm) cc_final: 0.8069 (tpt) REVERT: D 34 ASN cc_start: 0.6981 (OUTLIER) cc_final: 0.6510 (t0) REVERT: D 37 ASP cc_start: 0.6792 (m-30) cc_final: 0.6461 (m-30) REVERT: D 57 LYS cc_start: 0.8277 (tttp) cc_final: 0.8071 (ttpt) REVERT: D 68 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7624 (tp30) REVERT: D 94 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7377 (tm-30) REVERT: D 107 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8164 (mtmt) REVERT: D 181 SER cc_start: 0.8642 (t) cc_final: 0.8438 (t) REVERT: D 330 ASN cc_start: 0.9052 (m-40) cc_final: 0.8818 (m110) REVERT: E 34 ASN cc_start: 0.7170 (OUTLIER) cc_final: 0.6862 (t160) REVERT: E 81 LEU cc_start: 0.8800 (mt) cc_final: 0.8511 (mt) REVERT: E 107 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7751 (ttmt) REVERT: E 196 ASN cc_start: 0.8771 (p0) cc_final: 0.8427 (p0) REVERT: E 202 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7673 (mt0) REVERT: E 211 MET cc_start: 0.9097 (mtt) cc_final: 0.8816 (mtt) REVERT: E 243 MET cc_start: 0.9050 (mtm) cc_final: 0.8715 (mtt) REVERT: E 251 MET cc_start: 0.8280 (ttm) cc_final: 0.8079 (ttm) REVERT: E 272 GLN cc_start: 0.8518 (pt0) cc_final: 0.8250 (mt0) REVERT: E 296 SER cc_start: 0.8815 (p) cc_final: 0.8537 (m) REVERT: F 26 SER cc_start: 0.9037 (p) cc_final: 0.8799 (m) REVERT: F 39 LYS cc_start: 0.7952 (mttt) cc_final: 0.7403 (mtpp) REVERT: F 68 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8158 (mp0) REVERT: F 95 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8073 (ttp-110) REVERT: F 158 MET cc_start: 0.9055 (ttm) cc_final: 0.8816 (ttp) REVERT: F 202 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8028 (mt0) REVERT: F 206 GLN cc_start: 0.8854 (mt0) cc_final: 0.8503 (mt0) REVERT: F 253 LEU cc_start: 0.8913 (tp) cc_final: 0.8673 (tp) REVERT: G 39 LYS cc_start: 0.8363 (mttt) cc_final: 0.7928 (mtpp) REVERT: G 107 LYS cc_start: 0.7294 (mmtm) cc_final: 0.7081 (ttmm) REVERT: G 187 ASP cc_start: 0.8754 (m-30) cc_final: 0.8523 (m-30) REVERT: G 202 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8186 (mt0) REVERT: G 285 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8542 (ptmt) REVERT: G 308 GLU cc_start: 0.8295 (pm20) cc_final: 0.8087 (pm20) REVERT: H 27 ARG cc_start: 0.8046 (mtp-110) cc_final: 0.7366 (tmt170) REVERT: H 39 LYS cc_start: 0.8642 (mttt) cc_final: 0.8285 (mtpm) REVERT: H 94 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8390 (tp40) REVERT: H 125 MET cc_start: 0.8665 (mtp) cc_final: 0.8388 (mtm) REVERT: H 158 MET cc_start: 0.8720 (ttm) cc_final: 0.8329 (ttm) REVERT: H 187 ASP cc_start: 0.8631 (m-30) cc_final: 0.8408 (m-30) REVERT: H 254 ARG cc_start: 0.8386 (ttt-90) cc_final: 0.8103 (tmm-80) REVERT: I 27 ARG cc_start: 0.8444 (mtp-110) cc_final: 0.8224 (mtp-110) REVERT: I 33 ILE cc_start: 0.8221 (mm) cc_final: 0.7936 (mm) REVERT: I 39 LYS cc_start: 0.8739 (mttt) cc_final: 0.8394 (mmmm) REVERT: I 40 LYS cc_start: 0.8562 (mtpp) cc_final: 0.8065 (mtmm) REVERT: I 50 GLU cc_start: 0.8810 (mp0) cc_final: 0.8574 (mp0) REVERT: I 94 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8549 (tp40) REVERT: I 125 MET cc_start: 0.8812 (mtp) cc_final: 0.8498 (mtp) REVERT: I 223 SER cc_start: 0.9124 (t) cc_final: 0.8903 (t) REVERT: I 247 ARG cc_start: 0.8240 (mtp-110) cc_final: 0.8033 (mtp85) REVERT: I 285 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8684 (ptpt) REVERT: I 322 GLU cc_start: 0.7731 (tt0) cc_final: 0.7496 (tt0) REVERT: J 38 VAL cc_start: 0.8027 (t) cc_final: 0.7799 (m) REVERT: J 39 LYS cc_start: 0.8539 (mttt) cc_final: 0.7774 (mmmt) REVERT: J 40 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7632 (mtpt) REVERT: J 50 GLU cc_start: 0.8500 (mp0) cc_final: 0.8120 (mp0) REVERT: J 73 LYS cc_start: 0.6797 (mttt) cc_final: 0.6358 (tptt) REVERT: J 101 GLN cc_start: 0.8832 (mt0) cc_final: 0.8478 (mt0) REVERT: J 112 LEU cc_start: 0.8659 (tp) cc_final: 0.8446 (tp) REVERT: J 184 ASP cc_start: 0.7989 (m-30) cc_final: 0.7787 (m-30) REVERT: J 231 ASP cc_start: 0.8638 (m-30) cc_final: 0.8397 (m-30) REVERT: J 249 LEU cc_start: 0.9057 (mt) cc_final: 0.8793 (mp) REVERT: J 308 GLU cc_start: 0.7778 (pm20) cc_final: 0.7514 (mt-10) REVERT: J 332 ASP cc_start: 0.8251 (p0) cc_final: 0.8019 (p0) outliers start: 50 outliers final: 5 residues processed: 900 average time/residue: 1.6668 time to fit residues: 1698.8816 Evaluate side-chains 623 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 613 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain I residue 285 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 253 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 293 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 244 HIS A 330 ASN B 145 GLN B 202 GLN B 244 HIS C 23 GLN C 30 GLN C 145 GLN C 244 HIS D 30 GLN D 135 GLN D 202 GLN D 330 ASN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 HIS F 244 HIS J 34 ASN J 135 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26875 Z= 0.208 Angle : 0.484 6.646 36550 Z= 0.259 Chirality : 0.040 0.157 4139 Planarity : 0.003 0.035 4521 Dihedral : 14.143 148.161 4476 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.84 % Allowed : 17.68 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.13), residues: 3196 helix: -0.86 (0.13), residues: 1380 sheet: -1.43 (0.22), residues: 490 loop : -1.99 (0.14), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 244 PHE 0.011 0.001 PHE E 248 TYR 0.009 0.001 TYR C 228 ARG 0.007 0.001 ARG F 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 711 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7726 (m-30) cc_final: 0.7421 (m-30) REVERT: A 40 LYS cc_start: 0.7074 (mtpp) cc_final: 0.6521 (mtpt) REVERT: A 58 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7169 (mtpm) REVERT: A 68 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6241 (tm-30) REVERT: A 109 LEU cc_start: 0.8736 (tp) cc_final: 0.8418 (tp) REVERT: A 130 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.6566 (ptp90) REVERT: A 202 GLN cc_start: 0.8332 (mm-40) cc_final: 0.8074 (tt0) REVERT: A 254 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7845 (tmt90) REVERT: A 303 ARG cc_start: 0.7890 (mtp180) cc_final: 0.7671 (mtm180) REVERT: B 42 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7257 (mt-10) REVERT: B 43 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7236 (mt-10) REVERT: B 59 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7755 (tt0) REVERT: B 95 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7593 (ttt-90) REVERT: B 107 LYS cc_start: 0.8009 (mmtm) cc_final: 0.7454 (ptpt) REVERT: B 206 GLN cc_start: 0.7818 (mt0) cc_final: 0.7613 (mt0) REVERT: C 33 ILE cc_start: 0.8764 (mm) cc_final: 0.8428 (mm) REVERT: C 80 LYS cc_start: 0.7972 (mtmm) cc_final: 0.7610 (ttpp) REVERT: C 82 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8748 (p) REVERT: C 94 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7368 (tp40) REVERT: C 95 ARG cc_start: 0.8389 (ttp80) cc_final: 0.8014 (ttm170) REVERT: C 107 LYS cc_start: 0.8118 (mmtm) cc_final: 0.7729 (ptpp) REVERT: C 154 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7264 (mt-10) REVERT: C 187 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8390 (m-30) REVERT: C 202 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7780 (mt0) REVERT: C 216 TYR cc_start: 0.8933 (m-80) cc_final: 0.8662 (m-80) REVERT: C 308 GLU cc_start: 0.8489 (pm20) cc_final: 0.8172 (pm20) REVERT: D 34 ASN cc_start: 0.7121 (OUTLIER) cc_final: 0.6533 (t0) REVERT: D 37 ASP cc_start: 0.6934 (m-30) cc_final: 0.6517 (m-30) REVERT: D 57 LYS cc_start: 0.7997 (tttp) cc_final: 0.7733 (ttpt) REVERT: D 68 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7359 (tp30) REVERT: D 94 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7252 (tm-30) REVERT: D 107 LYS cc_start: 0.8387 (mmtm) cc_final: 0.8182 (mtmt) REVERT: D 187 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8457 (t70) REVERT: D 332 ASP cc_start: 0.9099 (p0) cc_final: 0.8836 (p0) REVERT: E 34 ASN cc_start: 0.6911 (OUTLIER) cc_final: 0.6392 (p0) REVERT: E 98 GLU cc_start: 0.8533 (tp30) cc_final: 0.8312 (mm-30) REVERT: E 107 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7854 (mtmt) REVERT: E 176 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8103 (tt0) REVERT: E 272 GLN cc_start: 0.8545 (pt0) cc_final: 0.8335 (mt0) REVERT: E 338 LYS cc_start: 0.8166 (tppp) cc_final: 0.7953 (ttmt) REVERT: F 39 LYS cc_start: 0.7507 (mttt) cc_final: 0.6643 (mtpp) REVERT: F 43 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7487 (mp0) REVERT: F 95 ARG cc_start: 0.8312 (ttp80) cc_final: 0.7991 (ttp-110) REVERT: F 187 ASP cc_start: 0.8615 (m-30) cc_final: 0.8388 (m-30) REVERT: F 202 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7744 (mt0) REVERT: F 215 ARG cc_start: 0.8354 (ttt90) cc_final: 0.8103 (ttp80) REVERT: G 39 LYS cc_start: 0.8118 (mttt) cc_final: 0.7729 (mtpp) REVERT: G 94 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7843 (tp-100) REVERT: G 107 LYS cc_start: 0.7236 (mmtm) cc_final: 0.6900 (ttmm) REVERT: G 176 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7749 (mm-30) REVERT: G 202 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7887 (mt0) REVERT: G 247 ARG cc_start: 0.8194 (mtp-110) cc_final: 0.7986 (mtp85) REVERT: G 300 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8244 (mp) REVERT: G 308 GLU cc_start: 0.8364 (pm20) cc_final: 0.8112 (pm20) REVERT: H 39 LYS cc_start: 0.8123 (mttt) cc_final: 0.7845 (mtpm) REVERT: H 66 ILE cc_start: 0.8496 (mm) cc_final: 0.8164 (mp) REVERT: H 94 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8288 (tp40) REVERT: H 96 ARG cc_start: 0.7862 (ttt90) cc_final: 0.7503 (ttt180) REVERT: H 205 TYR cc_start: 0.8773 (m-80) cc_final: 0.8511 (m-80) REVERT: H 247 ARG cc_start: 0.8124 (mtp-110) cc_final: 0.7753 (mmm160) REVERT: I 39 LYS cc_start: 0.8530 (mttt) cc_final: 0.8219 (mmmm) REVERT: I 40 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7828 (mtmm) REVERT: I 77 GLU cc_start: 0.8226 (tp30) cc_final: 0.8021 (tp30) REVERT: I 206 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8241 (mt0) REVERT: I 223 SER cc_start: 0.8968 (t) cc_final: 0.8659 (t) REVERT: J 39 LYS cc_start: 0.8075 (mttt) cc_final: 0.7245 (mmmt) REVERT: J 40 LYS cc_start: 0.7783 (mtpp) cc_final: 0.7262 (mtpt) REVERT: J 50 GLU cc_start: 0.8310 (mp0) cc_final: 0.8072 (mp0) REVERT: J 73 LYS cc_start: 0.6502 (mttt) cc_final: 0.5760 (tptt) REVERT: J 77 GLU cc_start: 0.7454 (mp0) cc_final: 0.6464 (mp0) REVERT: J 184 ASP cc_start: 0.8340 (m-30) cc_final: 0.8078 (m-30) REVERT: J 231 ASP cc_start: 0.8541 (m-30) cc_final: 0.8300 (m-30) REVERT: J 247 ARG cc_start: 0.7686 (mtp-110) cc_final: 0.7448 (ttm-80) REVERT: J 308 GLU cc_start: 0.7890 (pm20) cc_final: 0.7522 (mt-10) outliers start: 100 outliers final: 37 residues processed: 758 average time/residue: 1.5892 time to fit residues: 1372.0598 Evaluate side-chains 662 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 615 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 206 GLN Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 296 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 163 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 293 optimal weight: 0.9990 chunk 317 optimal weight: 30.0000 chunk 261 optimal weight: 10.0000 chunk 291 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 235 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 202 GLN C 272 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 HIS ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 26875 Z= 0.331 Angle : 0.531 8.569 36550 Z= 0.278 Chirality : 0.042 0.209 4139 Planarity : 0.004 0.049 4521 Dihedral : 14.199 144.850 4463 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.76 % Allowed : 20.56 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3196 helix: -0.05 (0.14), residues: 1310 sheet: -1.17 (0.22), residues: 490 loop : -1.45 (0.14), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 294 PHE 0.012 0.002 PHE I 92 TYR 0.014 0.001 TYR C 228 ARG 0.007 0.001 ARG E 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 633 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7843 (m-30) cc_final: 0.7599 (m-30) REVERT: A 40 LYS cc_start: 0.7136 (mtpp) cc_final: 0.6703 (mtpt) REVERT: A 58 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7373 (mtpm) REVERT: A 66 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.6986 (tt) REVERT: A 68 GLU cc_start: 0.6622 (mt-10) cc_final: 0.6178 (tm-30) REVERT: A 70 LYS cc_start: 0.6643 (ttpt) cc_final: 0.6432 (ttpt) REVERT: A 109 LEU cc_start: 0.8719 (tp) cc_final: 0.8429 (tp) REVERT: A 130 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7937 (ttp80) REVERT: A 145 GLN cc_start: 0.8657 (mt0) cc_final: 0.8277 (mp10) REVERT: A 187 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7968 (m-30) REVERT: A 202 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7995 (tt0) REVERT: A 206 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: A 254 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7678 (tmt90) REVERT: B 42 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7238 (mt-10) REVERT: B 43 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7339 (mt-10) REVERT: B 95 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7777 (ttt-90) REVERT: B 107 LYS cc_start: 0.7858 (mmtm) cc_final: 0.7188 (ptpt) REVERT: B 204 LEU cc_start: 0.9102 (mt) cc_final: 0.8795 (mt) REVERT: C 80 LYS cc_start: 0.7835 (mtmm) cc_final: 0.7485 (ttpp) REVERT: C 94 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7466 (tm-30) REVERT: C 95 ARG cc_start: 0.8391 (ttp80) cc_final: 0.7811 (ttp-170) REVERT: C 107 LYS cc_start: 0.8344 (mmtm) cc_final: 0.8005 (ptmt) REVERT: C 154 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7295 (mt-10) REVERT: C 181 SER cc_start: 0.8019 (t) cc_final: 0.7690 (p) REVERT: C 187 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8589 (m-30) REVERT: C 202 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7807 (mt0) REVERT: C 251 MET cc_start: 0.8701 (tpt) cc_final: 0.8232 (mtt) REVERT: C 308 GLU cc_start: 0.8578 (pm20) cc_final: 0.8259 (pm20) REVERT: D 27 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7503 (mtp180) REVERT: D 34 ASN cc_start: 0.7107 (OUTLIER) cc_final: 0.6481 (t0) REVERT: D 37 ASP cc_start: 0.7078 (m-30) cc_final: 0.6668 (m-30) REVERT: D 57 LYS cc_start: 0.7977 (tttp) cc_final: 0.7719 (ttpt) REVERT: D 68 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7682 (tp30) REVERT: D 72 ASP cc_start: 0.7824 (m-30) cc_final: 0.7381 (m-30) REVERT: D 94 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7174 (tm-30) REVERT: D 107 LYS cc_start: 0.8448 (mmtm) cc_final: 0.8198 (mtmt) REVERT: D 187 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8549 (t70) REVERT: D 247 ARG cc_start: 0.8256 (mtp-110) cc_final: 0.7985 (ttt-90) REVERT: E 34 ASN cc_start: 0.6754 (OUTLIER) cc_final: 0.6196 (p0) REVERT: E 68 GLU cc_start: 0.8313 (mp0) cc_final: 0.7642 (tp30) REVERT: E 107 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7928 (mtmt) REVERT: E 176 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8106 (tt0) REVERT: E 202 GLN cc_start: 0.8254 (mt0) cc_final: 0.7884 (mt0) REVERT: E 206 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7982 (mt0) REVERT: E 213 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8420 (mt-10) REVERT: E 272 GLN cc_start: 0.8634 (pt0) cc_final: 0.8314 (mt0) REVERT: E 338 LYS cc_start: 0.8013 (tppp) cc_final: 0.6780 (mptt) REVERT: F 39 LYS cc_start: 0.7520 (mttt) cc_final: 0.6790 (mtmt) REVERT: F 43 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7456 (mp0) REVERT: F 95 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7884 (ttp-110) REVERT: F 187 ASP cc_start: 0.8532 (m-30) cc_final: 0.8288 (m-30) REVERT: F 202 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7872 (mt0) REVERT: G 39 LYS cc_start: 0.8075 (mttt) cc_final: 0.7697 (mtpp) REVERT: G 91 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: G 94 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7893 (tp-100) REVERT: G 107 LYS cc_start: 0.7309 (mmtm) cc_final: 0.6904 (ttmm) REVERT: G 176 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7794 (mm-30) REVERT: G 202 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7900 (mt0) REVERT: G 300 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8206 (mt) REVERT: G 308 GLU cc_start: 0.8327 (pm20) cc_final: 0.8033 (pm20) REVERT: H 27 ARG cc_start: 0.8386 (ttt-90) cc_final: 0.7748 (ttm110) REVERT: H 39 LYS cc_start: 0.8142 (mttt) cc_final: 0.7831 (mtmm) REVERT: H 64 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6677 (ttmm) REVERT: H 94 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8240 (tp40) REVERT: H 215 ARG cc_start: 0.8170 (ttt90) cc_final: 0.7872 (ttt90) REVERT: H 247 ARG cc_start: 0.8208 (mtp-110) cc_final: 0.7800 (mmm160) REVERT: I 30 GLN cc_start: 0.8029 (mt0) cc_final: 0.7617 (mp10) REVERT: I 37 ASP cc_start: 0.8029 (m-30) cc_final: 0.7730 (m-30) REVERT: I 39 LYS cc_start: 0.8549 (mttt) cc_final: 0.8161 (mmmm) REVERT: I 40 LYS cc_start: 0.8341 (mtpp) cc_final: 0.7903 (mttp) REVERT: I 50 GLU cc_start: 0.8928 (mp0) cc_final: 0.8404 (mp0) REVERT: I 77 GLU cc_start: 0.8202 (tp30) cc_final: 0.7971 (tp30) REVERT: I 223 SER cc_start: 0.8962 (t) cc_final: 0.8622 (t) REVERT: I 247 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8206 (mtp85) REVERT: J 39 LYS cc_start: 0.8074 (mttt) cc_final: 0.7433 (mmmt) REVERT: J 40 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7617 (mtpt) REVERT: J 42 GLU cc_start: 0.7470 (tp30) cc_final: 0.6529 (tt0) REVERT: J 50 GLU cc_start: 0.8277 (mp0) cc_final: 0.7984 (mp0) REVERT: J 77 GLU cc_start: 0.7519 (mp0) cc_final: 0.7221 (mp0) REVERT: J 95 ARG cc_start: 0.8260 (ttp-170) cc_final: 0.7900 (ttm110) REVERT: J 109 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8668 (mp) REVERT: J 184 ASP cc_start: 0.8333 (m-30) cc_final: 0.7966 (m-30) REVERT: J 222 ASP cc_start: 0.8420 (t70) cc_final: 0.8202 (t0) REVERT: J 231 ASP cc_start: 0.8682 (m-30) cc_final: 0.8475 (m-30) REVERT: J 308 GLU cc_start: 0.7939 (pm20) cc_final: 0.7507 (mt-10) REVERT: J 316 ASP cc_start: 0.7822 (t0) cc_final: 0.7567 (t0) outliers start: 124 outliers final: 62 residues processed: 694 average time/residue: 1.6675 time to fit residues: 1313.6103 Evaluate side-chains 667 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 587 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 213 GLU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 261 VAL Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 247 ARG Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 261 VAL Chi-restraints excluded: chain J residue 272 GLN Chi-restraints excluded: chain J residue 296 SER Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 290 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 294 optimal weight: 0.9990 chunk 312 optimal weight: 0.0270 chunk 154 optimal weight: 4.9990 chunk 279 optimal weight: 20.0000 chunk 84 optimal weight: 0.7980 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 145 GLN B 202 GLN C 272 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 GLN J 94 GLN J 135 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26875 Z= 0.171 Angle : 0.454 7.504 36550 Z= 0.240 Chirality : 0.039 0.158 4139 Planarity : 0.003 0.036 4521 Dihedral : 13.878 144.388 4459 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.76 % Allowed : 22.25 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: -0.75 (0.14), residues: 3196 helix: 0.39 (0.14), residues: 1310 sheet: -0.90 (0.22), residues: 490 loop : -1.13 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 138 PHE 0.010 0.001 PHE C 248 TYR 0.015 0.001 TYR C 191 ARG 0.009 0.000 ARG I 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 628 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7163 (mtpp) cc_final: 0.6634 (mtpt) REVERT: A 66 ILE cc_start: 0.7408 (mm) cc_final: 0.7049 (tt) REVERT: A 68 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6266 (tm-30) REVERT: A 109 LEU cc_start: 0.8770 (tp) cc_final: 0.8454 (tp) REVERT: A 130 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7970 (ttp80) REVERT: A 206 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: A 211 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8223 (mtt) REVERT: A 254 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7724 (tmt90) REVERT: A 336 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7000 (m-30) REVERT: B 34 ASN cc_start: 0.6928 (OUTLIER) cc_final: 0.6232 (t0) REVERT: B 37 ASP cc_start: 0.7071 (m-30) cc_final: 0.6548 (m-30) REVERT: B 42 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7204 (mt-10) REVERT: B 43 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7325 (mt-10) REVERT: B 95 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7759 (ttt-90) REVERT: B 107 LYS cc_start: 0.7842 (mmtm) cc_final: 0.7294 (ptpt) REVERT: B 258 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7996 (mt-10) REVERT: B 336 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: C 80 LYS cc_start: 0.7873 (mtmm) cc_final: 0.7592 (ttpp) REVERT: C 82 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8649 (p) REVERT: C 94 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7336 (tm-30) REVERT: C 95 ARG cc_start: 0.8364 (ttp80) cc_final: 0.7943 (ttm170) REVERT: C 107 LYS cc_start: 0.8331 (mmtm) cc_final: 0.7994 (ptmt) REVERT: C 154 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7162 (mt-10) REVERT: C 181 SER cc_start: 0.8021 (t) cc_final: 0.7685 (p) REVERT: C 187 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8494 (m-30) REVERT: C 206 GLN cc_start: 0.7828 (mt0) cc_final: 0.7399 (mt0) REVERT: D 27 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7339 (mtp180) REVERT: D 34 ASN cc_start: 0.7152 (OUTLIER) cc_final: 0.6547 (t0) REVERT: D 37 ASP cc_start: 0.7111 (m-30) cc_final: 0.6746 (m-30) REVERT: D 57 LYS cc_start: 0.7934 (tttp) cc_final: 0.7716 (ttpt) REVERT: D 94 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7106 (tm-30) REVERT: D 107 LYS cc_start: 0.8412 (mmtm) cc_final: 0.8146 (mtmt) REVERT: D 187 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8580 (t70) REVERT: D 247 ARG cc_start: 0.8208 (mtp-110) cc_final: 0.8006 (ttt-90) REVERT: E 34 ASN cc_start: 0.6718 (OUTLIER) cc_final: 0.6147 (p0) REVERT: E 68 GLU cc_start: 0.8424 (mp0) cc_final: 0.7720 (tp30) REVERT: E 107 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7882 (mtmt) REVERT: E 176 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8047 (tt0) REVERT: E 202 GLN cc_start: 0.8179 (mt0) cc_final: 0.7775 (mt0) REVERT: E 213 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8433 (mt-10) REVERT: E 272 GLN cc_start: 0.8580 (pt0) cc_final: 0.8305 (mt0) REVERT: F 39 LYS cc_start: 0.7465 (mttt) cc_final: 0.6740 (mtmt) REVERT: F 43 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7430 (mp0) REVERT: F 95 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7873 (ttp-110) REVERT: F 202 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7861 (mt0) REVERT: G 39 LYS cc_start: 0.7906 (mttt) cc_final: 0.7523 (mtpp) REVERT: G 94 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7793 (tp-100) REVERT: G 107 LYS cc_start: 0.7534 (mmtm) cc_final: 0.6943 (ttmm) REVERT: G 176 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7802 (mm-30) REVERT: G 187 ASP cc_start: 0.8223 (m-30) cc_final: 0.7915 (m-30) REVERT: G 300 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8243 (mt) REVERT: G 306 ARG cc_start: 0.7432 (ttm110) cc_final: 0.6884 (ttp80) REVERT: G 308 GLU cc_start: 0.8271 (pm20) cc_final: 0.8007 (pm20) REVERT: H 27 ARG cc_start: 0.8259 (ttt-90) cc_final: 0.7584 (ttm110) REVERT: H 39 LYS cc_start: 0.8065 (mttt) cc_final: 0.7747 (mtmm) REVERT: H 43 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7920 (mt-10) REVERT: H 94 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8192 (tp40) REVERT: H 96 ARG cc_start: 0.7833 (ttt90) cc_final: 0.7580 (ttt180) REVERT: H 187 ASP cc_start: 0.8442 (m-30) cc_final: 0.8162 (m-30) REVERT: H 215 ARG cc_start: 0.8063 (ttt90) cc_final: 0.7685 (ttt90) REVERT: H 247 ARG cc_start: 0.8145 (mtp-110) cc_final: 0.7696 (mmm160) REVERT: I 28 LEU cc_start: 0.8571 (mt) cc_final: 0.8347 (mt) REVERT: I 30 GLN cc_start: 0.8032 (mt0) cc_final: 0.7645 (mp10) REVERT: I 37 ASP cc_start: 0.8000 (m-30) cc_final: 0.7688 (m-30) REVERT: I 39 LYS cc_start: 0.8438 (mttt) cc_final: 0.8080 (mmmm) REVERT: I 40 LYS cc_start: 0.8244 (mtpp) cc_final: 0.7836 (mttp) REVERT: I 50 GLU cc_start: 0.8847 (mp0) cc_final: 0.8458 (mp0) REVERT: I 145 GLN cc_start: 0.7792 (mt0) cc_final: 0.7580 (mt0) REVERT: I 223 SER cc_start: 0.8891 (t) cc_final: 0.8540 (t) REVERT: I 247 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8190 (mtp85) REVERT: J 39 LYS cc_start: 0.8049 (mttt) cc_final: 0.7367 (mmmt) REVERT: J 40 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7441 (mtpt) REVERT: J 42 GLU cc_start: 0.7520 (tp30) cc_final: 0.6540 (tt0) REVERT: J 50 GLU cc_start: 0.8130 (mp0) cc_final: 0.7859 (mp0) REVERT: J 77 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: J 95 ARG cc_start: 0.8212 (ttp-170) cc_final: 0.7926 (ttm110) REVERT: J 135 GLN cc_start: 0.8562 (mm-40) cc_final: 0.7464 (mp-120) REVERT: J 308 GLU cc_start: 0.7931 (pm20) cc_final: 0.7521 (mt-10) outliers start: 98 outliers final: 53 residues processed: 671 average time/residue: 1.6188 time to fit residues: 1236.8186 Evaluate side-chains 669 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 599 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 213 GLU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 247 ARG Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 296 SER Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 260 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 232 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 266 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 0.1980 chunk 280 optimal weight: 3.9990 chunk 78 optimal weight: 0.0970 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN D 145 GLN E 145 GLN G 202 GLN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26875 Z= 0.156 Angle : 0.445 7.152 36550 Z= 0.235 Chirality : 0.038 0.142 4139 Planarity : 0.003 0.044 4521 Dihedral : 13.657 143.473 4459 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.80 % Allowed : 22.94 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: -0.29 (0.14), residues: 3196 helix: 0.75 (0.14), residues: 1310 sheet: -0.19 (0.26), residues: 380 loop : -1.00 (0.14), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 138 PHE 0.011 0.001 PHE C 248 TYR 0.013 0.001 TYR C 191 ARG 0.009 0.000 ARG I 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 651 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.7152 (mtpp) cc_final: 0.6685 (mtpt) REVERT: A 68 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6174 (tm-30) REVERT: A 70 LYS cc_start: 0.6888 (ttpt) cc_final: 0.6570 (ttpt) REVERT: A 109 LEU cc_start: 0.8746 (tp) cc_final: 0.8424 (tp) REVERT: A 130 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7966 (ttp80) REVERT: A 206 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: A 211 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7946 (mtt) REVERT: A 254 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7713 (tmt90) REVERT: A 336 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.6985 (m-30) REVERT: B 34 ASN cc_start: 0.6722 (OUTLIER) cc_final: 0.6067 (t0) REVERT: B 37 ASP cc_start: 0.7033 (m-30) cc_final: 0.6520 (m-30) REVERT: B 42 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7174 (mt-10) REVERT: B 43 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7351 (mt-10) REVERT: B 95 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7730 (ttt-90) REVERT: B 107 LYS cc_start: 0.7838 (mmtm) cc_final: 0.7275 (ptpt) REVERT: C 80 LYS cc_start: 0.7760 (mtmm) cc_final: 0.7551 (ttpp) REVERT: C 82 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8652 (p) REVERT: C 94 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7327 (tm-30) REVERT: C 95 ARG cc_start: 0.8432 (ttp80) cc_final: 0.8034 (ttm170) REVERT: C 107 LYS cc_start: 0.8326 (mmtm) cc_final: 0.7986 (ptmt) REVERT: C 181 SER cc_start: 0.8125 (t) cc_final: 0.7870 (p) REVERT: C 187 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8451 (m-30) REVERT: D 27 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7202 (mtp180) REVERT: D 30 GLN cc_start: 0.7732 (mt0) cc_final: 0.7503 (mp10) REVERT: D 37 ASP cc_start: 0.7021 (m-30) cc_final: 0.6678 (m-30) REVERT: D 57 LYS cc_start: 0.7958 (tttp) cc_final: 0.7720 (ttpt) REVERT: D 94 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7248 (tm-30) REVERT: D 107 LYS cc_start: 0.8400 (mmtm) cc_final: 0.8129 (mtmt) REVERT: E 27 ARG cc_start: 0.8392 (mtp180) cc_final: 0.7767 (tpt-90) REVERT: E 34 ASN cc_start: 0.6725 (OUTLIER) cc_final: 0.6473 (p0) REVERT: E 57 LYS cc_start: 0.8435 (tptm) cc_final: 0.8008 (tttt) REVERT: E 68 GLU cc_start: 0.8350 (mp0) cc_final: 0.7666 (tp30) REVERT: E 107 LYS cc_start: 0.8142 (mmtm) cc_final: 0.7867 (mtmt) REVERT: E 145 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8644 (mp10) REVERT: E 176 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8036 (tt0) REVERT: E 202 GLN cc_start: 0.8206 (mt0) cc_final: 0.7840 (mt0) REVERT: E 213 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: E 243 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8592 (mtt) REVERT: E 272 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: E 338 LYS cc_start: 0.8070 (tppp) cc_final: 0.6778 (mptt) REVERT: F 39 LYS cc_start: 0.7444 (mttt) cc_final: 0.6674 (mtmt) REVERT: F 43 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7383 (mp0) REVERT: F 95 ARG cc_start: 0.8228 (ttp80) cc_final: 0.7877 (ttp-110) REVERT: F 187 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: F 202 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7846 (mt0) REVERT: G 39 LYS cc_start: 0.8027 (mttt) cc_final: 0.7646 (mtpp) REVERT: G 94 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7768 (tp-100) REVERT: G 107 LYS cc_start: 0.7754 (mmtm) cc_final: 0.7052 (ttmm) REVERT: G 150 ARG cc_start: 0.8280 (mtp85) cc_final: 0.8058 (mtp180) REVERT: G 176 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7789 (mm-30) REVERT: G 300 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8216 (mt) REVERT: G 306 ARG cc_start: 0.7468 (ttm110) cc_final: 0.6878 (ttp80) REVERT: G 308 GLU cc_start: 0.8208 (pm20) cc_final: 0.7914 (pm20) REVERT: H 27 ARG cc_start: 0.8142 (ttt-90) cc_final: 0.7460 (ttm110) REVERT: H 39 LYS cc_start: 0.8050 (mttt) cc_final: 0.7715 (mtmm) REVERT: H 94 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8183 (tp40) REVERT: H 95 ARG cc_start: 0.8001 (mtm180) cc_final: 0.7779 (mtm180) REVERT: H 96 ARG cc_start: 0.7893 (ttt90) cc_final: 0.7634 (ttt180) REVERT: H 187 ASP cc_start: 0.8389 (m-30) cc_final: 0.8021 (m-30) REVERT: H 206 GLN cc_start: 0.8840 (mt0) cc_final: 0.8585 (mt0) REVERT: H 247 ARG cc_start: 0.8132 (mtp-110) cc_final: 0.7663 (mmm160) REVERT: H 257 ASP cc_start: 0.8414 (m-30) cc_final: 0.8085 (m-30) REVERT: I 28 LEU cc_start: 0.8544 (mt) cc_final: 0.8322 (mt) REVERT: I 30 GLN cc_start: 0.8064 (mt0) cc_final: 0.7639 (mp10) REVERT: I 37 ASP cc_start: 0.7972 (m-30) cc_final: 0.7654 (m-30) REVERT: I 39 LYS cc_start: 0.8426 (mttt) cc_final: 0.8077 (mmmm) REVERT: I 40 LYS cc_start: 0.8284 (mtpp) cc_final: 0.7854 (mttp) REVERT: I 110 ASP cc_start: 0.8706 (m-30) cc_final: 0.8491 (m-30) REVERT: I 223 SER cc_start: 0.8868 (t) cc_final: 0.8498 (t) REVERT: I 273 VAL cc_start: 0.7925 (m) cc_final: 0.7512 (m) REVERT: J 39 LYS cc_start: 0.7981 (mttt) cc_final: 0.7385 (mmmt) REVERT: J 40 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7330 (mttt) REVERT: J 50 GLU cc_start: 0.8174 (mp0) cc_final: 0.7892 (mp0) REVERT: J 77 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: J 95 ARG cc_start: 0.8150 (ttp-170) cc_final: 0.7860 (ttm110) REVERT: J 215 ARG cc_start: 0.7547 (ttp80) cc_final: 0.6936 (tmt90) REVERT: J 308 GLU cc_start: 0.7895 (pm20) cc_final: 0.7527 (mt-10) outliers start: 99 outliers final: 53 residues processed: 686 average time/residue: 1.6183 time to fit residues: 1266.0436 Evaluate side-chains 689 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 619 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 272 GLN Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 213 GLU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 311 ILE Chi-restraints excluded: chain I residue 322 GLU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 105 optimal weight: 0.6980 chunk 281 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 312 optimal weight: 7.9990 chunk 259 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN H 290 ASN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 26875 Z= 0.306 Angle : 0.512 8.347 36550 Z= 0.268 Chirality : 0.041 0.181 4139 Planarity : 0.004 0.060 4521 Dihedral : 13.716 143.012 4456 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.79 % Allowed : 22.59 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: -0.24 (0.14), residues: 3196 helix: 0.81 (0.14), residues: 1310 sheet: -0.08 (0.27), residues: 380 loop : -1.03 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 294 PHE 0.021 0.001 PHE I 259 TYR 0.013 0.001 TYR G 315 ARG 0.016 0.001 ARG I 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 604 time to evaluate : 2.855 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8151 (m-30) cc_final: 0.7820 (m-30) REVERT: A 40 LYS cc_start: 0.7214 (mtpp) cc_final: 0.6727 (mtpt) REVERT: A 66 ILE cc_start: 0.7304 (OUTLIER) cc_final: 0.6857 (tt) REVERT: A 68 GLU cc_start: 0.6635 (mt-10) cc_final: 0.6141 (tm-30) REVERT: A 70 LYS cc_start: 0.6802 (ttpt) cc_final: 0.6583 (ttpt) REVERT: A 109 LEU cc_start: 0.8711 (tp) cc_final: 0.8418 (tp) REVERT: A 206 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7511 (mt0) REVERT: A 211 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8180 (mtt) REVERT: A 254 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7826 (tmt90) REVERT: A 336 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7228 (m-30) REVERT: B 34 ASN cc_start: 0.6918 (OUTLIER) cc_final: 0.6250 (t0) REVERT: B 37 ASP cc_start: 0.7171 (m-30) cc_final: 0.6626 (m-30) REVERT: B 42 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7178 (mt-10) REVERT: B 43 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7352 (mt-10) REVERT: B 95 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7795 (ttt-90) REVERT: B 107 LYS cc_start: 0.7841 (mmtm) cc_final: 0.7283 (ptpt) REVERT: B 336 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: C 82 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8633 (p) REVERT: C 94 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7452 (tm-30) REVERT: C 95 ARG cc_start: 0.8298 (ttp80) cc_final: 0.7886 (ttm170) REVERT: C 107 LYS cc_start: 0.8390 (mmtm) cc_final: 0.8045 (ptmt) REVERT: C 145 GLN cc_start: 0.8941 (mp10) cc_final: 0.8596 (mp10) REVERT: C 154 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7146 (mt-10) REVERT: C 181 SER cc_start: 0.8097 (t) cc_final: 0.7802 (p) REVERT: C 187 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8617 (m-30) REVERT: C 243 MET cc_start: 0.8559 (mtt) cc_final: 0.8301 (mtm) REVERT: C 251 MET cc_start: 0.8604 (tpt) cc_final: 0.8079 (mpt) REVERT: D 27 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7704 (mtp180) REVERT: D 57 LYS cc_start: 0.8006 (tttp) cc_final: 0.7745 (ttpt) REVERT: D 94 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7260 (tm-30) REVERT: D 107 LYS cc_start: 0.8425 (mmtm) cc_final: 0.8157 (mtmt) REVERT: D 272 GLN cc_start: 0.8526 (pt0) cc_final: 0.8210 (mt0) REVERT: E 68 GLU cc_start: 0.8361 (mp0) cc_final: 0.7685 (tp30) REVERT: E 107 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7838 (mtmt) REVERT: E 145 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8633 (mp10) REVERT: E 176 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8066 (tt0) REVERT: E 202 GLN cc_start: 0.8236 (mt0) cc_final: 0.7825 (mt0) REVERT: E 206 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7769 (mt0) REVERT: E 213 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8420 (mt-10) REVERT: E 272 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: F 39 LYS cc_start: 0.7731 (mttt) cc_final: 0.7022 (mtmt) REVERT: F 43 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7431 (mp0) REVERT: F 95 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7905 (ttp-110) REVERT: F 187 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8147 (m-30) REVERT: F 202 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7842 (mt0) REVERT: G 39 LYS cc_start: 0.8014 (mttt) cc_final: 0.7621 (mtpp) REVERT: G 40 LYS cc_start: 0.7619 (mtpp) cc_final: 0.7293 (mtmm) REVERT: G 91 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: G 94 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7776 (tp-100) REVERT: G 107 LYS cc_start: 0.7832 (mmtm) cc_final: 0.7163 (ttmm) REVERT: G 176 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7788 (mm-30) REVERT: G 206 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8516 (mt0) REVERT: G 300 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8223 (mt) REVERT: G 306 ARG cc_start: 0.7622 (ttm110) cc_final: 0.6939 (ttp80) REVERT: G 308 GLU cc_start: 0.8189 (pm20) cc_final: 0.7895 (pm20) REVERT: H 27 ARG cc_start: 0.8330 (ttt-90) cc_final: 0.7922 (tmt170) REVERT: H 39 LYS cc_start: 0.8076 (mttt) cc_final: 0.7688 (mtmm) REVERT: H 64 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6590 (ttmm) REVERT: H 94 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8160 (tp40) REVERT: H 96 ARG cc_start: 0.7886 (ttt90) cc_final: 0.7615 (ttt180) REVERT: H 187 ASP cc_start: 0.8475 (m-30) cc_final: 0.8126 (m-30) REVERT: H 206 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8517 (mt0) REVERT: H 247 ARG cc_start: 0.8192 (mtp-110) cc_final: 0.7731 (mmm160) REVERT: I 27 ARG cc_start: 0.7604 (ttm110) cc_final: 0.7197 (ttt-90) REVERT: I 30 GLN cc_start: 0.8026 (mt0) cc_final: 0.7649 (mp10) REVERT: I 37 ASP cc_start: 0.7996 (m-30) cc_final: 0.7589 (m-30) REVERT: I 39 LYS cc_start: 0.8424 (mttt) cc_final: 0.8027 (mmmm) REVERT: I 40 LYS cc_start: 0.8355 (mtpp) cc_final: 0.7934 (mttp) REVERT: I 50 GLU cc_start: 0.8793 (mp0) cc_final: 0.8289 (mp0) REVERT: I 223 SER cc_start: 0.8930 (t) cc_final: 0.8548 (t) REVERT: J 39 LYS cc_start: 0.7843 (mttt) cc_final: 0.7197 (mmmt) REVERT: J 40 LYS cc_start: 0.8065 (mtpp) cc_final: 0.7405 (mttt) REVERT: J 42 GLU cc_start: 0.7657 (tp30) cc_final: 0.7418 (tp30) REVERT: J 50 GLU cc_start: 0.8246 (mp0) cc_final: 0.7950 (mp0) REVERT: J 77 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: J 80 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7578 (mttp) REVERT: J 215 ARG cc_start: 0.7623 (ttp80) cc_final: 0.7375 (ttp80) REVERT: J 308 GLU cc_start: 0.7927 (pm20) cc_final: 0.7470 (mt-10) outliers start: 125 outliers final: 68 residues processed: 652 average time/residue: 1.6421 time to fit residues: 1215.7528 Evaluate side-chains 674 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 584 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 336 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 213 GLU Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 322 GLU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 80 LYS Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 176 optimal weight: 0.0070 chunk 263 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 311 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 202 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN G 202 GLN H 290 ASN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26875 Z= 0.210 Angle : 0.475 7.734 36550 Z= 0.250 Chirality : 0.039 0.147 4139 Planarity : 0.003 0.047 4521 Dihedral : 13.677 143.654 4454 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.91 % Allowed : 23.67 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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 (0.14), residues: 3196 helix: 0.95 (0.14), residues: 1310 sheet: -0.05 (0.26), residues: 380 loop : -0.91 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 294 PHE 0.015 0.001 PHE I 259 TYR 0.022 0.001 TYR C 191 ARG 0.013 0.001 ARG I 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 606 time to evaluate : 2.779 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8214 (m-30) cc_final: 0.7857 (m-30) REVERT: A 40 LYS cc_start: 0.7201 (mtpp) cc_final: 0.6716 (mtpt) REVERT: A 68 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6012 (tm-30) REVERT: A 70 LYS cc_start: 0.7084 (ttpt) cc_final: 0.6791 (ttpt) REVERT: A 109 LEU cc_start: 0.8776 (tp) cc_final: 0.8430 (tp) REVERT: A 206 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7504 (mt0) REVERT: A 211 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8192 (mtt) REVERT: A 254 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7826 (tmt90) REVERT: A 336 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7200 (m-30) REVERT: B 34 ASN cc_start: 0.6778 (OUTLIER) cc_final: 0.6042 (t0) REVERT: B 37 ASP cc_start: 0.7198 (m-30) cc_final: 0.6649 (m-30) REVERT: B 42 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7002 (mt-10) REVERT: B 43 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7345 (mt-10) REVERT: B 77 GLU cc_start: 0.7258 (mp0) cc_final: 0.6964 (mm-30) REVERT: B 95 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7761 (ttt-90) REVERT: B 107 LYS cc_start: 0.7852 (mmtm) cc_final: 0.7279 (ptpt) REVERT: B 336 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: C 82 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8645 (p) REVERT: C 94 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7320 (tm-30) REVERT: C 95 ARG cc_start: 0.8418 (ttp80) cc_final: 0.7840 (ttp-170) REVERT: C 107 LYS cc_start: 0.8380 (mmtm) cc_final: 0.8037 (ptmt) REVERT: C 145 GLN cc_start: 0.8882 (mp10) cc_final: 0.8518 (mp10) REVERT: C 154 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7075 (mt-10) REVERT: C 181 SER cc_start: 0.8084 (t) cc_final: 0.7795 (p) REVERT: C 187 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8580 (m-30) REVERT: C 243 MET cc_start: 0.8476 (mtt) cc_final: 0.8207 (mtm) REVERT: C 251 MET cc_start: 0.8651 (tpt) cc_final: 0.8116 (mpt) REVERT: D 27 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7265 (mtp180) REVERT: D 30 GLN cc_start: 0.7778 (mt0) cc_final: 0.7517 (mp10) REVERT: D 57 LYS cc_start: 0.7971 (tttp) cc_final: 0.7733 (ttpt) REVERT: D 94 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7180 (tm-30) REVERT: D 107 LYS cc_start: 0.8420 (mmtm) cc_final: 0.8157 (mtmt) REVERT: D 272 GLN cc_start: 0.8492 (pt0) cc_final: 0.8203 (mt0) REVERT: E 68 GLU cc_start: 0.8412 (mp0) cc_final: 0.7821 (tp30) REVERT: E 107 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7832 (mtmt) REVERT: E 145 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8635 (mp10) REVERT: E 202 GLN cc_start: 0.8202 (mt0) cc_final: 0.7841 (mt0) REVERT: E 206 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7742 (mt0) REVERT: E 213 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8416 (mt-10) REVERT: E 272 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8302 (mt0) REVERT: E 338 LYS cc_start: 0.8027 (tppp) cc_final: 0.6736 (mptt) REVERT: F 27 ARG cc_start: 0.8736 (mtp180) cc_final: 0.8127 (ttt-90) REVERT: F 39 LYS cc_start: 0.7693 (mttt) cc_final: 0.6981 (mtmt) REVERT: F 43 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7483 (mp0) REVERT: F 95 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7891 (ttp-110) REVERT: F 187 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8141 (m-30) REVERT: F 202 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7831 (mt0) REVERT: G 39 LYS cc_start: 0.7860 (mttt) cc_final: 0.7452 (mtpp) REVERT: G 91 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: G 94 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7779 (tp-100) REVERT: G 107 LYS cc_start: 0.7970 (mmtm) cc_final: 0.7234 (ttmm) REVERT: G 176 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7790 (mm-30) REVERT: G 300 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8241 (mt) REVERT: G 306 ARG cc_start: 0.7517 (ttm110) cc_final: 0.6899 (ttp80) REVERT: G 308 GLU cc_start: 0.8170 (pm20) cc_final: 0.7854 (pm20) REVERT: H 27 ARG cc_start: 0.8226 (ttt-90) cc_final: 0.7830 (tmt170) REVERT: H 39 LYS cc_start: 0.8052 (mttt) cc_final: 0.7741 (mtmm) REVERT: H 94 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8129 (tp40) REVERT: H 96 ARG cc_start: 0.7918 (ttt90) cc_final: 0.7689 (ttt180) REVERT: H 187 ASP cc_start: 0.8470 (m-30) cc_final: 0.8073 (m-30) REVERT: H 206 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8493 (mt0) REVERT: H 247 ARG cc_start: 0.8154 (mtp-110) cc_final: 0.7681 (mmm160) REVERT: I 27 ARG cc_start: 0.7465 (ttm110) cc_final: 0.6974 (ttt-90) REVERT: I 30 GLN cc_start: 0.7973 (mt0) cc_final: 0.7578 (mp10) REVERT: I 37 ASP cc_start: 0.8001 (m-30) cc_final: 0.7584 (m-30) REVERT: I 39 LYS cc_start: 0.8406 (mttt) cc_final: 0.8045 (mmmm) REVERT: I 40 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7919 (mttp) REVERT: I 50 GLU cc_start: 0.8755 (mp0) cc_final: 0.8261 (mp0) REVERT: I 223 SER cc_start: 0.8863 (t) cc_final: 0.8496 (t) REVERT: J 39 LYS cc_start: 0.7797 (mttt) cc_final: 0.7241 (mmmt) REVERT: J 40 LYS cc_start: 0.8100 (mtpp) cc_final: 0.7449 (mttt) REVERT: J 42 GLU cc_start: 0.7690 (tp30) cc_final: 0.7455 (tp30) REVERT: J 50 GLU cc_start: 0.8187 (mp0) cc_final: 0.7893 (mp0) REVERT: J 77 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: J 177 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8073 (ttt180) REVERT: J 215 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7323 (ttp80) REVERT: J 308 GLU cc_start: 0.7930 (pm20) cc_final: 0.7470 (mt-10) outliers start: 102 outliers final: 60 residues processed: 649 average time/residue: 1.6321 time to fit residues: 1202.1998 Evaluate side-chains 667 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 587 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 213 GLU Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 322 GLU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 177 ARG Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 215 ARG Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 296 SER Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 192 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 197 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN C 30 GLN C 101 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN H 34 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 GLN H 290 ASN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26875 Z= 0.225 Angle : 0.483 7.846 36550 Z= 0.253 Chirality : 0.039 0.176 4139 Planarity : 0.003 0.041 4521 Dihedral : 13.673 142.815 4454 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.26 % Allowed : 23.40 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: 0.02 (0.14), residues: 3196 helix: 1.02 (0.14), residues: 1310 sheet: 0.01 (0.26), residues: 380 loop : -0.86 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 138 PHE 0.015 0.001 PHE I 259 TYR 0.026 0.001 TYR C 191 ARG 0.011 0.001 ARG I 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 592 time to evaluate : 3.108 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8165 (m-30) cc_final: 0.7821 (m-30) REVERT: A 40 LYS cc_start: 0.7205 (mtpp) cc_final: 0.6720 (mtpt) REVERT: A 68 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6122 (tm-30) REVERT: A 70 LYS cc_start: 0.6968 (ttpt) cc_final: 0.6696 (ttpt) REVERT: A 109 LEU cc_start: 0.8778 (tp) cc_final: 0.8435 (tp) REVERT: A 206 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7524 (mt0) REVERT: A 211 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8005 (mtt) REVERT: A 254 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7844 (tmt90) REVERT: A 336 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: B 34 ASN cc_start: 0.6738 (OUTLIER) cc_final: 0.6059 (t0) REVERT: B 37 ASP cc_start: 0.7202 (m-30) cc_final: 0.6658 (m-30) REVERT: B 42 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7085 (mt-10) REVERT: B 43 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7360 (mt-10) REVERT: B 95 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7752 (ttt-90) REVERT: B 107 LYS cc_start: 0.7851 (mmtm) cc_final: 0.7280 (ptpt) REVERT: B 336 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: C 82 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8637 (p) REVERT: C 94 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7321 (tm-30) REVERT: C 95 ARG cc_start: 0.8411 (ttp80) cc_final: 0.7836 (ttp-170) REVERT: C 107 LYS cc_start: 0.8423 (mmtm) cc_final: 0.8045 (ptmt) REVERT: C 145 GLN cc_start: 0.8894 (mp10) cc_final: 0.8532 (mp10) REVERT: C 154 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7072 (mt-10) REVERT: C 181 SER cc_start: 0.8018 (t) cc_final: 0.7758 (p) REVERT: C 187 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8547 (m-30) REVERT: C 251 MET cc_start: 0.8656 (tpt) cc_final: 0.8130 (mpt) REVERT: C 255 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8734 (tp) REVERT: D 27 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7306 (mtp180) REVERT: D 30 GLN cc_start: 0.7787 (mt0) cc_final: 0.7527 (mp10) REVERT: D 57 LYS cc_start: 0.7981 (tttp) cc_final: 0.7711 (ttpt) REVERT: D 81 LEU cc_start: 0.8691 (mt) cc_final: 0.8470 (mt) REVERT: D 94 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7240 (tm-30) REVERT: D 107 LYS cc_start: 0.8424 (mmtm) cc_final: 0.8158 (mtmt) REVERT: D 272 GLN cc_start: 0.8513 (pt0) cc_final: 0.8244 (mt0) REVERT: E 27 ARG cc_start: 0.8323 (mtp180) cc_final: 0.8016 (ttt-90) REVERT: E 68 GLU cc_start: 0.8408 (mp0) cc_final: 0.7831 (tp30) REVERT: E 107 LYS cc_start: 0.8146 (mmtm) cc_final: 0.7851 (mtmt) REVERT: E 202 GLN cc_start: 0.8195 (mt0) cc_final: 0.7783 (mt0) REVERT: E 272 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8260 (mt0) REVERT: E 338 LYS cc_start: 0.8019 (tppp) cc_final: 0.6722 (mptt) REVERT: F 39 LYS cc_start: 0.7678 (mttt) cc_final: 0.6992 (mtmt) REVERT: F 43 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7452 (mp0) REVERT: F 95 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7892 (ttp-110) REVERT: F 187 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: F 202 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7831 (mt0) REVERT: F 254 ARG cc_start: 0.7935 (ttt-90) cc_final: 0.7707 (ttp-170) REVERT: G 39 LYS cc_start: 0.7866 (mttt) cc_final: 0.7462 (mtpp) REVERT: G 91 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: G 94 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7784 (tp-100) REVERT: G 107 LYS cc_start: 0.8072 (mmtm) cc_final: 0.7253 (ttmm) REVERT: G 176 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7775 (mm-30) REVERT: G 211 MET cc_start: 0.8606 (mtt) cc_final: 0.8127 (mtt) REVERT: G 300 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8241 (mt) REVERT: G 306 ARG cc_start: 0.7533 (ttm110) cc_final: 0.6906 (ttp80) REVERT: G 308 GLU cc_start: 0.8163 (pm20) cc_final: 0.7864 (pm20) REVERT: H 27 ARG cc_start: 0.8249 (ttt-90) cc_final: 0.7859 (tmt170) REVERT: H 39 LYS cc_start: 0.8114 (mttt) cc_final: 0.7743 (mtmm) REVERT: H 94 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8160 (tp40) REVERT: H 96 ARG cc_start: 0.7921 (ttt90) cc_final: 0.7696 (ttt180) REVERT: H 187 ASP cc_start: 0.8501 (m-30) cc_final: 0.8112 (m-30) REVERT: H 206 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8502 (mt0) REVERT: H 247 ARG cc_start: 0.8160 (mtp-110) cc_final: 0.7681 (mmm160) REVERT: I 27 ARG cc_start: 0.7409 (ttm110) cc_final: 0.7106 (ttt-90) REVERT: I 37 ASP cc_start: 0.8007 (m-30) cc_final: 0.7559 (m-30) REVERT: I 39 LYS cc_start: 0.8414 (mttt) cc_final: 0.8026 (mmmm) REVERT: I 40 LYS cc_start: 0.8311 (mtpp) cc_final: 0.7925 (mttp) REVERT: I 50 GLU cc_start: 0.8755 (mp0) cc_final: 0.8259 (mp0) REVERT: I 184 ASP cc_start: 0.7733 (m-30) cc_final: 0.7062 (t0) REVERT: J 39 LYS cc_start: 0.7827 (mttt) cc_final: 0.7241 (mmmt) REVERT: J 40 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7450 (mttt) REVERT: J 50 GLU cc_start: 0.8168 (mp0) cc_final: 0.7875 (mp0) REVERT: J 77 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: J 177 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8102 (ttt180) REVERT: J 215 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7432 (ttp80) REVERT: J 308 GLU cc_start: 0.7930 (pm20) cc_final: 0.7476 (mt-10) outliers start: 111 outliers final: 71 residues processed: 639 average time/residue: 1.6559 time to fit residues: 1199.9159 Evaluate side-chains 674 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 585 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 322 GLU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 177 ARG Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 215 ARG Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 261 VAL Chi-restraints excluded: chain J residue 296 SER Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 283 optimal weight: 0.3980 chunk 298 optimal weight: 10.0000 chunk 272 optimal weight: 3.9990 chunk 290 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 262 optimal weight: 0.9980 chunk 274 optimal weight: 2.9990 chunk 289 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN G 202 GLN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 290 ASN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26875 Z= 0.177 Angle : 0.465 7.721 36550 Z= 0.244 Chirality : 0.039 0.134 4139 Planarity : 0.003 0.041 4521 Dihedral : 13.623 142.626 4454 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.49 % Allowed : 24.40 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: 0.15 (0.14), residues: 3196 helix: 1.12 (0.14), residues: 1310 sheet: 0.09 (0.27), residues: 380 loop : -0.78 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 138 PHE 0.014 0.001 PHE I 259 TYR 0.022 0.001 TYR C 191 ARG 0.010 0.001 ARG I 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 612 time to evaluate : 2.968 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8316 (m-30) cc_final: 0.7919 (m-30) REVERT: A 40 LYS cc_start: 0.7283 (mtpp) cc_final: 0.6822 (mtpt) REVERT: A 68 GLU cc_start: 0.6628 (mt-10) cc_final: 0.6030 (tm-30) REVERT: A 70 LYS cc_start: 0.7039 (ttpt) cc_final: 0.6788 (ttpt) REVERT: A 206 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: A 336 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.6998 (m-30) REVERT: B 34 ASN cc_start: 0.6750 (OUTLIER) cc_final: 0.6039 (t0) REVERT: B 37 ASP cc_start: 0.7187 (m-30) cc_final: 0.6645 (m-30) REVERT: B 42 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6830 (mt-10) REVERT: B 43 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7324 (mt-10) REVERT: B 95 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7768 (ttt-90) REVERT: B 107 LYS cc_start: 0.7838 (mmtm) cc_final: 0.7273 (ptpt) REVERT: B 187 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.7923 (m-30) REVERT: B 336 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: C 82 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8611 (p) REVERT: C 94 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7308 (tm-30) REVERT: C 95 ARG cc_start: 0.8375 (ttp80) cc_final: 0.7616 (ttp-170) REVERT: C 107 LYS cc_start: 0.8412 (mmtm) cc_final: 0.8035 (ptmt) REVERT: C 145 GLN cc_start: 0.8801 (mp10) cc_final: 0.8444 (mp10) REVERT: C 154 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7080 (mt-10) REVERT: C 181 SER cc_start: 0.8000 (t) cc_final: 0.7713 (p) REVERT: C 187 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8465 (m-30) REVERT: C 251 MET cc_start: 0.8663 (tpt) cc_final: 0.8140 (mpt) REVERT: D 27 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7000 (mtp180) REVERT: D 94 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7250 (tm-30) REVERT: D 107 LYS cc_start: 0.8415 (mmtm) cc_final: 0.8150 (mtmt) REVERT: D 272 GLN cc_start: 0.8457 (pt0) cc_final: 0.8205 (mt0) REVERT: D 306 ARG cc_start: 0.7427 (ttp-110) cc_final: 0.7157 (ttm110) REVERT: E 57 LYS cc_start: 0.8490 (tptm) cc_final: 0.8011 (tttt) REVERT: E 68 GLU cc_start: 0.8399 (mp0) cc_final: 0.7832 (tp30) REVERT: E 107 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7844 (mtmt) REVERT: E 145 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8572 (mp10) REVERT: E 176 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8023 (tt0) REVERT: E 202 GLN cc_start: 0.8203 (mt0) cc_final: 0.7804 (mt0) REVERT: E 272 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8293 (mt0) REVERT: E 338 LYS cc_start: 0.7832 (tppp) cc_final: 0.6561 (mptt) REVERT: F 27 ARG cc_start: 0.8711 (mtp180) cc_final: 0.8265 (ttt-90) REVERT: F 39 LYS cc_start: 0.7575 (mttt) cc_final: 0.6871 (mtmt) REVERT: F 43 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7419 (mp0) REVERT: F 119 THR cc_start: 0.8942 (t) cc_final: 0.8608 (t) REVERT: F 187 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: F 202 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7831 (mt0) REVERT: F 254 ARG cc_start: 0.7904 (ttt-90) cc_final: 0.7702 (ttp-170) REVERT: G 39 LYS cc_start: 0.7845 (mttt) cc_final: 0.7552 (mtpm) REVERT: G 94 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7756 (tp-100) REVERT: G 107 LYS cc_start: 0.8061 (mmtm) cc_final: 0.7254 (ttmm) REVERT: G 124 GLU cc_start: 0.8801 (tt0) cc_final: 0.8569 (tt0) REVERT: G 176 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7760 (mm-30) REVERT: G 300 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8257 (mt) REVERT: G 306 ARG cc_start: 0.7532 (ttm110) cc_final: 0.6901 (ttp80) REVERT: G 308 GLU cc_start: 0.8154 (pm20) cc_final: 0.7861 (pm20) REVERT: H 27 ARG cc_start: 0.8194 (ttt-90) cc_final: 0.7796 (tmt170) REVERT: H 39 LYS cc_start: 0.8092 (mttt) cc_final: 0.7723 (mtmm) REVERT: H 94 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8143 (tp40) REVERT: H 96 ARG cc_start: 0.7887 (ttt90) cc_final: 0.7662 (ttt180) REVERT: H 187 ASP cc_start: 0.8425 (m-30) cc_final: 0.8003 (m-30) REVERT: H 247 ARG cc_start: 0.8136 (mtp-110) cc_final: 0.7750 (mmm160) REVERT: H 257 ASP cc_start: 0.8431 (m-30) cc_final: 0.8197 (m-30) REVERT: I 27 ARG cc_start: 0.7347 (ttm110) cc_final: 0.7116 (ttt-90) REVERT: I 37 ASP cc_start: 0.8002 (m-30) cc_final: 0.7553 (m-30) REVERT: I 39 LYS cc_start: 0.8404 (mttt) cc_final: 0.8051 (mmmm) REVERT: I 40 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7915 (mttp) REVERT: I 184 ASP cc_start: 0.7737 (m-30) cc_final: 0.7094 (t0) REVERT: J 39 LYS cc_start: 0.8051 (mttt) cc_final: 0.7450 (mmmt) REVERT: J 40 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7440 (mttt) REVERT: J 42 GLU cc_start: 0.7774 (tp30) cc_final: 0.6707 (tt0) REVERT: J 50 GLU cc_start: 0.8145 (mp0) cc_final: 0.7875 (mp0) REVERT: J 77 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: J 177 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7974 (ttt180) REVERT: J 215 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7153 (tmt90) REVERT: J 308 GLU cc_start: 0.7925 (pm20) cc_final: 0.7481 (mt-10) REVERT: J 316 ASP cc_start: 0.7923 (t0) cc_final: 0.7714 (t0) REVERT: J 332 ASP cc_start: 0.8276 (p0) cc_final: 0.7970 (p0) outliers start: 91 outliers final: 70 residues processed: 649 average time/residue: 1.6337 time to fit residues: 1204.4594 Evaluate side-chains 675 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 589 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 311 ILE Chi-restraints excluded: chain I residue 322 GLU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 177 ARG Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 215 ARG Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 261 VAL Chi-restraints excluded: chain J residue 296 SER Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 190 optimal weight: 1.9990 chunk 306 optimal weight: 7.9990 chunk 187 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 321 optimal weight: 8.9990 chunk 296 optimal weight: 4.9990 chunk 256 optimal weight: 0.7980 chunk 26 optimal weight: 0.0470 chunk 197 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN G 202 GLN H 34 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 290 ASN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26875 Z= 0.170 Angle : 0.467 10.767 36550 Z= 0.245 Chirality : 0.039 0.135 4139 Planarity : 0.003 0.043 4521 Dihedral : 13.581 142.034 4454 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.45 % Allowed : 24.86 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: 0.27 (0.15), residues: 3196 helix: 1.28 (0.15), residues: 1290 sheet: 0.13 (0.27), residues: 380 loop : -0.75 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 138 PHE 0.011 0.001 PHE F 126 TYR 0.022 0.001 TYR C 191 ARG 0.010 0.001 ARG A 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6392 Ramachandran restraints generated. 3196 Oldfield, 0 Emsley, 3196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 611 time to evaluate : 2.516 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8258 (m-30) cc_final: 0.7925 (m-30) REVERT: A 40 LYS cc_start: 0.7296 (mtpp) cc_final: 0.6835 (mtpt) REVERT: A 68 GLU cc_start: 0.6531 (mt-10) cc_final: 0.6118 (tm-30) REVERT: A 206 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7646 (mt0) REVERT: A 336 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.6997 (m-30) REVERT: B 34 ASN cc_start: 0.6703 (OUTLIER) cc_final: 0.6048 (t0) REVERT: B 37 ASP cc_start: 0.7183 (m-30) cc_final: 0.6645 (m-30) REVERT: B 42 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6824 (mt-10) REVERT: B 43 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7332 (mt-10) REVERT: B 95 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7792 (ttt-90) REVERT: B 107 LYS cc_start: 0.7828 (mmtm) cc_final: 0.7267 (ptpt) REVERT: B 187 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7896 (m-30) REVERT: B 274 ASP cc_start: 0.5577 (t0) cc_final: 0.5024 (p0) REVERT: B 336 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: C 82 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8539 (p) REVERT: C 94 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7302 (tm-30) REVERT: C 95 ARG cc_start: 0.8374 (ttp80) cc_final: 0.7624 (ttp-170) REVERT: C 107 LYS cc_start: 0.8411 (mmtm) cc_final: 0.8037 (ptmt) REVERT: C 145 GLN cc_start: 0.8812 (mp10) cc_final: 0.8463 (mp10) REVERT: C 154 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7089 (mt-10) REVERT: C 181 SER cc_start: 0.8163 (t) cc_final: 0.7850 (p) REVERT: C 187 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8465 (m-30) REVERT: C 206 GLN cc_start: 0.7961 (mt0) cc_final: 0.7454 (mm-40) REVERT: C 251 MET cc_start: 0.8664 (tpt) cc_final: 0.8146 (mpt) REVERT: D 27 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7010 (mtp180) REVERT: D 94 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7249 (tm-30) REVERT: D 107 LYS cc_start: 0.8394 (mmtm) cc_final: 0.8158 (mtmt) REVERT: D 181 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8289 (p) REVERT: D 272 GLN cc_start: 0.8435 (pt0) cc_final: 0.8190 (mt0) REVERT: D 306 ARG cc_start: 0.7413 (ttp-110) cc_final: 0.7141 (ttm110) REVERT: E 27 ARG cc_start: 0.8242 (ttt-90) cc_final: 0.7537 (tpt-90) REVERT: E 57 LYS cc_start: 0.8487 (tptm) cc_final: 0.8010 (tttt) REVERT: E 68 GLU cc_start: 0.8398 (mp0) cc_final: 0.7830 (tp30) REVERT: E 107 LYS cc_start: 0.8082 (mmtm) cc_final: 0.7824 (mtmt) REVERT: E 145 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8551 (mp10) REVERT: E 176 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7988 (tt0) REVERT: E 202 GLN cc_start: 0.8211 (mt0) cc_final: 0.7808 (mt0) REVERT: E 272 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8293 (mt0) REVERT: E 338 LYS cc_start: 0.7841 (tppp) cc_final: 0.6566 (mptt) REVERT: F 39 LYS cc_start: 0.7559 (mttt) cc_final: 0.6830 (mtmt) REVERT: F 43 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7353 (mp0) REVERT: F 119 THR cc_start: 0.8947 (t) cc_final: 0.8602 (t) REVERT: F 187 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8138 (m-30) REVERT: F 202 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7844 (mt0) REVERT: F 254 ARG cc_start: 0.7900 (ttt-90) cc_final: 0.7690 (ttp-170) REVERT: G 39 LYS cc_start: 0.7850 (mttt) cc_final: 0.7434 (mtpp) REVERT: G 94 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7751 (tp-100) REVERT: G 107 LYS cc_start: 0.8068 (mmtm) cc_final: 0.7253 (ttmm) REVERT: G 176 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7781 (mm-30) REVERT: G 300 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8243 (mt) REVERT: G 306 ARG cc_start: 0.7534 (ttm110) cc_final: 0.6899 (ttp80) REVERT: G 308 GLU cc_start: 0.8153 (pm20) cc_final: 0.7859 (pm20) REVERT: H 27 ARG cc_start: 0.8124 (ttt-90) cc_final: 0.7731 (tmt170) REVERT: H 39 LYS cc_start: 0.8101 (mttt) cc_final: 0.7682 (mtmm) REVERT: H 94 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8101 (tp40) REVERT: H 96 ARG cc_start: 0.7883 (ttt90) cc_final: 0.7663 (ttt180) REVERT: H 187 ASP cc_start: 0.8391 (m-30) cc_final: 0.7956 (m-30) REVERT: H 247 ARG cc_start: 0.8128 (mtp-110) cc_final: 0.7743 (mmm160) REVERT: H 257 ASP cc_start: 0.8370 (m-30) cc_final: 0.8091 (m-30) REVERT: H 258 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8309 (mt-10) REVERT: I 37 ASP cc_start: 0.7994 (m-30) cc_final: 0.7556 (m-30) REVERT: I 39 LYS cc_start: 0.8406 (mttt) cc_final: 0.7972 (mmmm) REVERT: I 40 LYS cc_start: 0.8248 (mtpp) cc_final: 0.7917 (mttp) REVERT: I 48 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8767 (p) REVERT: I 75 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8339 (mt) REVERT: I 184 ASP cc_start: 0.7615 (m-30) cc_final: 0.6948 (t0) REVERT: I 306 ARG cc_start: 0.7447 (ptm-80) cc_final: 0.6985 (ttp-170) REVERT: J 39 LYS cc_start: 0.8043 (mttt) cc_final: 0.7446 (mmmt) REVERT: J 40 LYS cc_start: 0.8096 (mtpp) cc_final: 0.7396 (mttt) REVERT: J 42 GLU cc_start: 0.7772 (tp30) cc_final: 0.6686 (tt0) REVERT: J 50 GLU cc_start: 0.8128 (mp0) cc_final: 0.7869 (mp0) REVERT: J 77 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: J 177 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8033 (ttt180) REVERT: J 215 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7226 (tmt90) REVERT: J 308 GLU cc_start: 0.7916 (pm20) cc_final: 0.7471 (mt-10) outliers start: 90 outliers final: 61 residues processed: 646 average time/residue: 1.6292 time to fit residues: 1197.9053 Evaluate side-chains 679 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 599 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 145 GLN Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 272 GLN Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 272 GLN Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 311 ILE Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 177 ARG Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 215 ARG Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 261 VAL Chi-restraints excluded: chain J residue 296 SER Chi-restraints excluded: chain J residue 322 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 203 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 71 optimal weight: 7.9990 chunk 256 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 ASN C 30 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN G 23 GLN G 202 GLN H 34 ASN H 200 GLN H 244 HIS H 290 ASN ** I 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.110267 restraints weight = 32306.975| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.95 r_work: 0.3052 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26875 Z= 0.338 Angle : 0.548 10.602 36550 Z= 0.285 Chirality : 0.042 0.174 4139 Planarity : 0.004 0.051 4521 Dihedral : 13.744 140.832 4454 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.68 % Allowed : 25.12 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3196 helix: 1.04 (0.14), residues: 1290 sheet: 0.09 (0.26), residues: 380 loop : -0.83 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 294 PHE 0.024 0.001 PHE I 259 TYR 0.023 0.002 TYR C 191 ARG 0.011 0.001 ARG A 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16237.77 seconds wall clock time: 288 minutes 52.16 seconds (17332.16 seconds total)