Starting phenix.real_space_refine on Fri Mar 15 20:13:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/03_2024/6he4_0209_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/03_2024/6he4_0209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/03_2024/6he4_0209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/03_2024/6he4_0209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/03_2024/6he4_0209_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/03_2024/6he4_0209_updated.pdb" } resolution = 4.85 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= 0.002 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 P 14 5.49 5 Mg 5 5.21 5 S 42 5.16 5 C 8042 2.51 5 N 2161 2.21 5 O 2420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "H TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 147": "OD1" <-> "OD2" Residue "H PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 225": "OE1" <-> "OE2" Residue "H PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 232": "OE1" <-> "OE2" Residue "H GLU 242": "OE1" <-> "OE2" Residue "H ASP 258": "OD1" <-> "OD2" Residue "H ASP 273": "OD1" <-> "OD2" Residue "H PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 276": "OD1" <-> "OD2" Residue "H ASP 280": "OD1" <-> "OD2" Residue "H GLU 315": "OE1" <-> "OE2" Residue "H PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 332": "OE1" <-> "OE2" Residue "H PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 357": "OE1" <-> "OE2" Residue "H GLU 366": "OE1" <-> "OE2" Residue "H ASP 374": "OD1" <-> "OD2" Residue "H GLU 380": "OE1" <-> "OE2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 131": "OE1" <-> "OE2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "I TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 147": "OD1" <-> "OD2" Residue "I GLU 152": "OE1" <-> "OE2" Residue "I GLU 158": "OE1" <-> "OE2" Residue "I TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 241": "OD1" <-> "OD2" Residue "I ASP 244": "OD1" <-> "OD2" Residue "I ASP 258": "OD1" <-> "OD2" Residue "I ARG 259": "NH1" <-> "NH2" Residue "I ASP 273": "OD1" <-> "OD2" Residue "I ASP 276": "OD1" <-> "OD2" Residue "I ASP 280": "OD1" <-> "OD2" Residue "I ASP 291": "OD1" <-> "OD2" Residue "I ASP 294": "OD1" <-> "OD2" Residue "I PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 304": "OD1" <-> "OD2" Residue "I GLU 308": "OE1" <-> "OE2" Residue "I GLU 315": "OE1" <-> "OE2" Residue "I PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 332": "OE1" <-> "OE2" Residue "I ASP 335": "OD1" <-> "OD2" Residue "I GLU 338": "OE1" <-> "OE2" Residue "I GLU 344": "OE1" <-> "OE2" Residue "I PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 380": "OE1" <-> "OE2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "K GLU 137": "OE1" <-> "OE2" Residue "K TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 141": "OE1" <-> "OE2" Residue "K ASP 142": "OD1" <-> "OD2" Residue "K ASP 147": "OD1" <-> "OD2" Residue "K GLU 152": "OE1" <-> "OE2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "K GLU 158": "OE1" <-> "OE2" Residue "K GLU 169": "OE1" <-> "OE2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "K TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 210": "OE1" <-> "OE2" Residue "K PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 218": "OE1" <-> "OE2" Residue "K GLU 225": "OE1" <-> "OE2" Residue "K ASP 241": "OD1" <-> "OD2" Residue "K GLU 242": "OE1" <-> "OE2" Residue "K ASP 254": "OD1" <-> "OD2" Residue "K ASP 258": "OD1" <-> "OD2" Residue "K ASP 294": "OD1" <-> "OD2" Residue "K PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 304": "OD1" <-> "OD2" Residue "K GLU 308": "OE1" <-> "OE2" Residue "K PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 332": "OE1" <-> "OE2" Residue "K GLU 357": "OE1" <-> "OE2" Residue "K PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 366": "OE1" <-> "OE2" Residue "K GLU 380": "OE1" <-> "OE2" Residue "L ASP 124": "OD1" <-> "OD2" Residue "L TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 134": "OE1" <-> "OE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L ASP 142": "OD1" <-> "OD2" Residue "L GLU 151": "OE1" <-> "OE2" Residue "L GLU 152": "OE1" <-> "OE2" Residue "L GLU 158": "OE1" <-> "OE2" Residue "L GLU 173": "OE1" <-> "OE2" Residue "L TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 210": "OE1" <-> "OE2" Residue "L GLU 232": "OE1" <-> "OE2" Residue "L ASP 241": "OD1" <-> "OD2" Residue "L ASP 244": "OD1" <-> "OD2" Residue "L ASP 273": "OD1" <-> "OD2" Residue "L ASP 280": "OD1" <-> "OD2" Residue "L ASP 304": "OD1" <-> "OD2" Residue "L GLU 308": "OE1" <-> "OE2" Residue "L PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 344": "OE1" <-> "OE2" Residue "L ASP 350": "OD1" <-> "OD2" Residue "L GLU 357": "OE1" <-> "OE2" Residue "M TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 141": "OE1" <-> "OE2" Residue "M GLU 152": "OE1" <-> "OE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M GLU 158": "OE1" <-> "OE2" Residue "M PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 169": "OE1" <-> "OE2" Residue "M GLU 173": "OE1" <-> "OE2" Residue "M TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 210": "OE1" <-> "OE2" Residue "M GLU 218": "OE1" <-> "OE2" Residue "M GLU 225": "OE1" <-> "OE2" Residue "M PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 232": "OE1" <-> "OE2" Residue "M GLU 242": "OE1" <-> "OE2" Residue "M ASP 258": "OD1" <-> "OD2" Residue "M GLU 260": "OE1" <-> "OE2" Residue "M PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 304": "OD1" <-> "OD2" Residue "M GLU 308": "OE1" <-> "OE2" Residue "M PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 332": "OE1" <-> "OE2" Residue "M PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 350": "OD1" <-> "OD2" Residue "M GLU 357": "OE1" <-> "OE2" Residue "M PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 365": "OE1" <-> "OE2" Residue "M GLU 366": "OE1" <-> "OE2" Residue "M PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 380": "OE1" <-> "OE2" Residue "J ASP 124": "OD1" <-> "OD2" Residue "J PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 131": "OE1" <-> "OE2" Residue "J TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 147": "OD1" <-> "OD2" Residue "J GLU 151": "OE1" <-> "OE2" Residue "J GLU 152": "OE1" <-> "OE2" Residue "J GLU 173": "OE1" <-> "OE2" Residue "J GLU 232": "OE1" <-> "OE2" Residue "J GLU 242": "OE1" <-> "OE2" Residue "J ASP 244": "OD1" <-> "OD2" Residue "J ASP 254": "OD1" <-> "OD2" Residue "J ASP 258": "OD1" <-> "OD2" Residue "J GLU 260": "OE1" <-> "OE2" Residue "J GLU 271": "OE1" <-> "OE2" Residue "J ASP 276": "OD1" <-> "OD2" Residue "J ASP 304": "OD1" <-> "OD2" Residue "J PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 332": "OE1" <-> "OE2" Residue "J ASP 333": "OD1" <-> "OD2" Residue "J PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 350": "OD1" <-> "OD2" Residue "J PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 366": "OE1" <-> "OE2" Residue "J PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12684 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 247} Chain: "I" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 248} Chain: "K" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "L" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 249} Chain: "M" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 249} Chain: "J" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 6, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 245} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.19, per 1000 atoms: 0.57 Number of scatterers: 12684 At special positions: 0 Unit cell: (134, 128.64, 80.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 14 15.00 Mg 5 11.99 O 2420 8.00 N 2161 7.00 C 8042 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: 4.96 Conformation dependent library (CDL) restraints added in 2.2 seconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2964 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 10 sheets defined 45.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'H' and resid 125 through 130 removed outlier: 3.935A pdb=" N PHE H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 156 removed outlier: 3.610A pdb=" N GLU H 152 " --> pdb=" O VAL H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 162 Processing helix chain 'H' and resid 164 through 170 Processing helix chain 'H' and resid 188 through 199 Processing helix chain 'H' and resid 220 through 232 removed outlier: 3.879A pdb=" N PHE H 227 " --> pdb=" O VAL H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 274 removed outlier: 3.530A pdb=" N LEU H 269 " --> pdb=" O MET H 265 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU H 271 " --> pdb=" O GLN H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 327 removed outlier: 3.809A pdb=" N ILE H 318 " --> pdb=" O PHE H 314 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 342 removed outlier: 3.520A pdb=" N ARG H 341 " --> pdb=" O LYS H 337 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE H 342 " --> pdb=" O GLU H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 365 Processing helix chain 'H' and resid 372 through 384 Processing helix chain 'I' and resid 125 through 128 No H-bonds generated for 'chain 'I' and resid 125 through 128' Processing helix chain 'I' and resid 148 through 162 removed outlier: 3.789A pdb=" N LEU I 159 " --> pdb=" O GLU I 155 " (cutoff:3.500A) Proline residue: I 160 - end of helix Processing helix chain 'I' and resid 164 through 170 removed outlier: 3.541A pdb=" N VAL I 170 " --> pdb=" O LEU I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 199 removed outlier: 3.721A pdb=" N ASN I 197 " --> pdb=" O LYS I 193 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN I 198 " --> pdb=" O ALA I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 232 removed outlier: 3.690A pdb=" N LEU I 222 " --> pdb=" O GLU I 218 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU I 232 " --> pdb=" O GLN I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 243 through 245 No H-bonds generated for 'chain 'I' and resid 243 through 245' Processing helix chain 'I' and resid 259 through 272 removed outlier: 3.847A pdb=" N GLN I 267 " --> pdb=" O ARG I 263 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA I 270 " --> pdb=" O MET I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 298 No H-bonds generated for 'chain 'I' and resid 295 through 298' Processing helix chain 'I' and resid 314 through 327 removed outlier: 3.769A pdb=" N ILE I 318 " --> pdb=" O PHE I 314 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS I 327 " --> pdb=" O ILE I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 342 Processing helix chain 'I' and resid 348 through 364 Processing helix chain 'I' and resid 372 through 386 removed outlier: 3.652A pdb=" N LYS I 381 " --> pdb=" O LYS I 377 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL I 382 " --> pdb=" O ALA I 378 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS I 385 " --> pdb=" O LYS I 381 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR I 386 " --> pdb=" O VAL I 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 162 removed outlier: 3.660A pdb=" N GLU K 152 " --> pdb=" O VAL K 148 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL K 157 " --> pdb=" O ILE K 153 " (cutoff:3.500A) Proline residue: K 160 - end of helix Processing helix chain 'K' and resid 164 through 170 removed outlier: 3.644A pdb=" N ALA K 168 " --> pdb=" O PRO K 164 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU K 169 " --> pdb=" O GLU K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 198 Processing helix chain 'K' and resid 218 through 232 Processing helix chain 'K' and resid 262 through 268 removed outlier: 3.962A pdb=" N GLN K 267 " --> pdb=" O ARG K 263 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 298 No H-bonds generated for 'chain 'K' and resid 295 through 298' Processing helix chain 'K' and resid 314 through 327 removed outlier: 3.532A pdb=" N HIS K 324 " --> pdb=" O ILE K 320 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS K 327 " --> pdb=" O ILE K 323 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 342 removed outlier: 3.561A pdb=" N ILE K 342 " --> pdb=" O GLU K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 348 through 364 Processing helix chain 'K' and resid 372 through 384 Processing helix chain 'L' and resid 125 through 130 removed outlier: 5.490A pdb=" N PHE L 130 " --> pdb=" O MET L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 156 removed outlier: 3.523A pdb=" N GLU L 152 " --> pdb=" O VAL L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 162 No H-bonds generated for 'chain 'L' and resid 159 through 162' Processing helix chain 'L' and resid 164 through 170 removed outlier: 3.864A pdb=" N GLU L 169 " --> pdb=" O LEU L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 199 Processing helix chain 'L' and resid 218 through 232 removed outlier: 3.521A pdb=" N VAL L 223 " --> pdb=" O GLY L 219 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 273 removed outlier: 4.097A pdb=" N ARG L 259 " --> pdb=" O THR L 255 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU L 260 " --> pdb=" O SER L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 298 No H-bonds generated for 'chain 'L' and resid 295 through 298' Processing helix chain 'L' and resid 314 through 326 removed outlier: 3.841A pdb=" N ILE L 318 " --> pdb=" O PHE L 314 " (cutoff:3.500A) Processing helix chain 'L' and resid 337 through 343 removed outlier: 3.978A pdb=" N ILE L 342 " --> pdb=" O GLU L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 348 through 365 removed outlier: 3.512A pdb=" N CYS L 355 " --> pdb=" O ILE L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 384 Processing helix chain 'M' and resid 147 through 156 removed outlier: 3.847A pdb=" N GLU M 151 " --> pdb=" O ASP M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 162 Processing helix chain 'M' and resid 164 through 169 removed outlier: 3.768A pdb=" N GLU M 169 " --> pdb=" O LEU M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 199 Processing helix chain 'M' and resid 219 through 233 removed outlier: 4.015A pdb=" N VAL M 223 " --> pdb=" O GLY M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 274 removed outlier: 3.692A pdb=" N GLU M 260 " --> pdb=" O SER M 256 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL M 261 " --> pdb=" O GLY M 257 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN M 267 " --> pdb=" O ARG M 263 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU M 268 " --> pdb=" O THR M 264 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU M 271 " --> pdb=" O GLN M 267 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP M 273 " --> pdb=" O LEU M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 314 through 325 removed outlier: 3.833A pdb=" N ILE M 323 " --> pdb=" O GLN M 319 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS M 324 " --> pdb=" O ILE M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 336 through 342 Processing helix chain 'M' and resid 348 through 364 removed outlier: 3.644A pdb=" N GLY M 359 " --> pdb=" O CYS M 355 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET M 360 " --> pdb=" O THR M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 372 through 382 Processing helix chain 'J' and resid 127 through 130 No H-bonds generated for 'chain 'J' and resid 127 through 130' Processing helix chain 'J' and resid 147 through 156 Processing helix chain 'J' and resid 158 through 162 Processing helix chain 'J' and resid 164 through 170 removed outlier: 3.801A pdb=" N VAL J 170 " --> pdb=" O PHE J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 199 removed outlier: 3.883A pdb=" N GLN J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 232 Processing helix chain 'J' and resid 243 through 246 No H-bonds generated for 'chain 'J' and resid 243 through 246' Processing helix chain 'J' and resid 261 through 272 removed outlier: 3.600A pdb=" N LEU J 269 " --> pdb=" O MET J 266 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU J 271 " --> pdb=" O LEU J 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 298 No H-bonds generated for 'chain 'J' and resid 295 through 298' Processing helix chain 'J' and resid 314 through 327 removed outlier: 3.678A pdb=" N ILE J 318 " --> pdb=" O PHE J 314 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE J 323 " --> pdb=" O GLN J 319 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS J 324 " --> pdb=" O ILE J 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 348 through 364 Processing helix chain 'J' and resid 372 through 384 Processing sheet with id= A, first strand: chain 'H' and resid 178 through 181 removed outlier: 6.645A pdb=" N ARG H 305 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N TYR H 181 " --> pdb=" O ARG H 305 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE H 307 " --> pdb=" O TYR H 181 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'H' and resid 237 through 240 removed outlier: 6.784A pdb=" N LYS H 282 " --> pdb=" O ILE H 238 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ILE H 240 " --> pdb=" O LYS H 282 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE H 284 " --> pdb=" O ILE H 240 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'I' and resid 283 through 287 removed outlier: 3.673A pdb=" N TYR I 181 " --> pdb=" O ILE I 307 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'I' and resid 203 through 206 removed outlier: 6.750A pdb=" N ILE I 237 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL I 206 " --> pdb=" O ILE I 237 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N PHE I 239 " --> pdb=" O VAL I 206 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'K' and resid 305 through 308 removed outlier: 3.581A pdb=" N ARG K 305 " --> pdb=" O GLY K 177 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR K 181 " --> pdb=" O ILE K 307 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL K 283 " --> pdb=" O VAL K 178 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU K 180 " --> pdb=" O VAL K 283 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY K 285 " --> pdb=" O LEU K 180 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE K 284 " --> pdb=" O SER K 236 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE K 238 " --> pdb=" O ILE K 284 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA K 286 " --> pdb=" O ILE K 238 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE K 240 " --> pdb=" O ALA K 286 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR K 202 " --> pdb=" O ILE K 237 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE K 239 " --> pdb=" O THR K 202 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE K 204 " --> pdb=" O PHE K 239 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASP K 241 " --> pdb=" O ILE K 204 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL K 206 " --> pdb=" O ASP K 241 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 178 through 181 removed outlier: 6.472A pdb=" N ARG L 305 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TYR L 181 " --> pdb=" O ARG L 305 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE L 307 " --> pdb=" O TYR L 181 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'L' and resid 202 through 207 removed outlier: 3.506A pdb=" N ASP L 241 " --> pdb=" O VAL L 206 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'M' and resid 132 through 134 removed outlier: 3.647A pdb=" N LYS M 282 " --> pdb=" O SER M 236 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE M 238 " --> pdb=" O LYS M 282 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL M 178 " --> pdb=" O GLY M 285 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ARG M 305 " --> pdb=" O LEU M 179 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N TYR M 181 " --> pdb=" O ARG M 305 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE M 307 " --> pdb=" O TYR M 181 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'J' and resid 283 through 287 removed outlier: 3.722A pdb=" N THR J 287 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG J 305 " --> pdb=" O LEU J 179 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N TYR J 181 " --> pdb=" O ARG J 305 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE J 307 " --> pdb=" O TYR J 181 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 202 through 206 420 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.30: 2235 1.30 - 1.45: 3773 1.45 - 1.60: 6582 1.60 - 1.75: 210 1.75 - 1.90: 81 Bond restraints: 12881 Sorted by residual: bond pdb=" O3A ATP J 401 " pdb=" PB ATP J 401 " ideal model delta sigma weight residual 1.592 1.786 -0.194 1.10e-02 8.26e+03 3.11e+02 bond pdb=" O3A ATP K 401 " pdb=" PB ATP K 401 " ideal model delta sigma weight residual 1.592 1.764 -0.172 1.10e-02 8.26e+03 2.45e+02 bond pdb=" CA VAL H 206 " pdb=" C VAL H 206 " ideal model delta sigma weight residual 1.523 1.381 0.141 1.17e-02 7.31e+03 1.46e+02 bond pdb=" N ALA L 353 " pdb=" CA ALA L 353 " ideal model delta sigma weight residual 1.459 1.314 0.145 1.23e-02 6.61e+03 1.40e+02 bond pdb=" O3A ATP I 401 " pdb=" PB ATP I 401 " ideal model delta sigma weight residual 1.592 1.716 -0.124 1.10e-02 8.26e+03 1.26e+02 ... (remaining 12876 not shown) Histogram of bond angle deviations from ideal: 82.45 - 97.73: 30 97.73 - 113.02: 5940 113.02 - 128.30: 11149 128.30 - 143.58: 280 143.58 - 158.87: 8 Bond angle restraints: 17407 Sorted by residual: angle pdb=" PA ATP K 401 " pdb=" O3A ATP K 401 " pdb=" PB ATP K 401 " ideal model delta sigma weight residual 136.83 158.87 -22.04 1.00e+00 1.00e+00 4.86e+02 angle pdb=" PA ATP H 401 " pdb=" O3A ATP H 401 " pdb=" PB ATP H 401 " ideal model delta sigma weight residual 136.83 158.43 -21.60 1.00e+00 1.00e+00 4.66e+02 angle pdb=" PB ATP I 401 " pdb=" O3B ATP I 401 " pdb=" PG ATP I 401 " ideal model delta sigma weight residual 139.87 158.05 -18.18 1.00e+00 1.00e+00 3.30e+02 angle pdb=" PB ATP J 401 " pdb=" O3B ATP J 401 " pdb=" PG ATP J 401 " ideal model delta sigma weight residual 139.87 157.49 -17.62 1.00e+00 1.00e+00 3.10e+02 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 156.19 -16.32 1.00e+00 1.00e+00 2.66e+02 ... (remaining 17402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.64: 7567 28.64 - 57.28: 358 57.28 - 85.92: 124 85.92 - 114.56: 15 114.56 - 143.20: 3 Dihedral angle restraints: 8067 sinusoidal: 3483 harmonic: 4584 Sorted by residual: dihedral pdb=" CA GLU H 218 " pdb=" C GLU H 218 " pdb=" N GLY H 219 " pdb=" CA GLY H 219 " ideal model delta harmonic sigma weight residual -180.00 -45.34 -134.66 0 5.00e+00 4.00e-02 7.25e+02 dihedral pdb=" CA ASP I 254 " pdb=" C ASP I 254 " pdb=" N THR I 255 " pdb=" CA THR I 255 " ideal model delta harmonic sigma weight residual 180.00 45.62 134.38 0 5.00e+00 4.00e-02 7.22e+02 dihedral pdb=" CA ILE H 240 " pdb=" C ILE H 240 " pdb=" N ASP H 241 " pdb=" CA ASP H 241 " ideal model delta harmonic sigma weight residual -180.00 -86.63 -93.37 0 5.00e+00 4.00e-02 3.49e+02 ... (remaining 8064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 1148 0.161 - 0.323: 632 0.323 - 0.484: 164 0.484 - 0.645: 50 0.645 - 0.806: 6 Chirality restraints: 2000 Sorted by residual: chirality pdb=" CA LYS K 282 " pdb=" N LYS K 282 " pdb=" C LYS K 282 " pdb=" CB LYS K 282 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" CB VAL I 195 " pdb=" CA VAL I 195 " pdb=" CG1 VAL I 195 " pdb=" CG2 VAL I 195 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" CA PHE I 361 " pdb=" N PHE I 361 " pdb=" C PHE I 361 " pdb=" CB PHE I 361 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 1997 not shown) Planarity restraints: 2243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP K 401 " 0.191 2.00e-02 2.50e+03 1.12e-01 3.43e+02 pdb=" C2 ATP K 401 " -0.047 2.00e-02 2.50e+03 pdb=" C4 ATP K 401 " -0.039 2.00e-02 2.50e+03 pdb=" C5 ATP K 401 " -0.130 2.00e-02 2.50e+03 pdb=" C6 ATP K 401 " -0.057 2.00e-02 2.50e+03 pdb=" C8 ATP K 401 " -0.026 2.00e-02 2.50e+03 pdb=" N1 ATP K 401 " 0.029 2.00e-02 2.50e+03 pdb=" N3 ATP K 401 " -0.039 2.00e-02 2.50e+03 pdb=" N6 ATP K 401 " 0.238 2.00e-02 2.50e+03 pdb=" N7 ATP K 401 " -0.131 2.00e-02 2.50e+03 pdb=" N9 ATP K 401 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 128 " 0.250 2.00e-02 2.50e+03 1.30e-01 3.39e+02 pdb=" CG TYR I 128 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TYR I 128 " -0.121 2.00e-02 2.50e+03 pdb=" CD2 TYR I 128 " -0.122 2.00e-02 2.50e+03 pdb=" CE1 TYR I 128 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR I 128 " -0.064 2.00e-02 2.50e+03 pdb=" CZ TYR I 128 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR I 128 " 0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 215 " 0.220 2.00e-02 2.50e+03 1.16e-01 2.70e+02 pdb=" CG TYR H 215 " -0.129 2.00e-02 2.50e+03 pdb=" CD1 TYR H 215 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR H 215 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR H 215 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR H 215 " -0.063 2.00e-02 2.50e+03 pdb=" CZ TYR H 215 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR H 215 " 0.165 2.00e-02 2.50e+03 ... (remaining 2240 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 117 2.54 - 3.13: 8703 3.13 - 3.72: 19217 3.72 - 4.31: 29096 4.31 - 4.90: 46035 Nonbonded interactions: 103168 Sorted by model distance: nonbonded pdb=" O2G ATP I 401 " pdb="MG MG I 402 " model vdw 1.953 2.170 nonbonded pdb=" O2G ATP K 401 " pdb="MG MG K 402 " model vdw 1.998 2.170 nonbonded pdb=" O2G ATP H 401 " pdb="MG MG H 402 " model vdw 1.999 2.170 nonbonded pdb=" O2B ATP K 401 " pdb="MG MG K 402 " model vdw 2.103 2.170 nonbonded pdb=" O2B ATP I 401 " pdb="MG MG I 402 " model vdw 2.153 2.170 ... (remaining 103163 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 'H' and resid 123 through 389) selection = (chain 'I' and resid 123 through 389) selection = (chain 'J' and resid 123 through 389) selection = (chain 'K' and resid 123 through 389) selection = (chain 'L' and resid 123 through 389) selection = chain 'M' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 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: 0.010 Extract box with map and model: 11.980 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 36.530 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 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 : 0.036 0.205 12881 Z= 2.339 Angle : 3.648 27.314 17407 Z= 2.465 Chirality : 0.208 0.806 2000 Planarity : 0.031 0.256 2243 Dihedral : 19.331 143.201 5103 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 4.09 % Allowed : 6.42 % Favored : 89.50 % Rotamer: Outliers : 3.66 % Allowed : 9.12 % Favored : 87.22 % Cbeta Deviations : 7.49 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 1.13 % Twisted Proline : 5.56 % Twisted General : 1.66 % 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: -2.84 (0.18), residues: 1590 helix: -1.19 (0.16), residues: 763 sheet: -1.00 (0.37), residues: 141 loop : -2.88 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.037 0.016 HIS L 324 PHE 0.167 0.040 PHE I 167 TYR 0.250 0.051 TYR I 128 ARG 0.079 0.011 ARG J 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 827 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 179 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8371 (mt) REVERT: H 229 LEU cc_start: 0.8759 (tp) cc_final: 0.8347 (tp) REVERT: H 268 LEU cc_start: 0.7203 (tp) cc_final: 0.6920 (tp) REVERT: H 269 LEU cc_start: 0.8934 (mt) cc_final: 0.8614 (mp) REVERT: H 336 PHE cc_start: 0.6879 (m-80) cc_final: 0.6645 (m-80) REVERT: H 337 LYS cc_start: 0.7673 (mtpp) cc_final: 0.7446 (mtmt) REVERT: H 354 ILE cc_start: 0.8837 (mt) cc_final: 0.8551 (mt) REVERT: H 361 PHE cc_start: 0.5084 (t80) cc_final: 0.4410 (t80) REVERT: H 363 ILE cc_start: 0.8560 (mt) cc_final: 0.8303 (mt) REVERT: H 373 LEU cc_start: 0.7768 (tp) cc_final: 0.7284 (tp) REVERT: H 379 ILE cc_start: 0.8435 (mt) cc_final: 0.8095 (mt) REVERT: I 127 VAL cc_start: 0.6647 (m) cc_final: 0.5630 (m) REVERT: I 150 ILE cc_start: 0.7193 (mt) cc_final: 0.6375 (mt) REVERT: I 159 LEU cc_start: 0.8150 (tp) cc_final: 0.7895 (tp) REVERT: I 184 PRO cc_start: 0.8121 (Cg_exo) cc_final: 0.7807 (Cg_endo) REVERT: I 186 THR cc_start: 0.7500 (p) cc_final: 0.7152 (p) REVERT: I 207 VAL cc_start: 0.8451 (t) cc_final: 0.7529 (t) REVERT: I 231 LYS cc_start: 0.8767 (mttm) cc_final: 0.8554 (mmmt) REVERT: I 294 ASP cc_start: 0.8610 (m-30) cc_final: 0.8316 (t0) REVERT: I 297 ILE cc_start: 0.8608 (mp) cc_final: 0.7972 (mp) REVERT: I 309 VAL cc_start: 0.9142 (t) cc_final: 0.8718 (p) REVERT: I 320 ILE cc_start: 0.8850 (mt) cc_final: 0.8584 (mm) REVERT: I 370 VAL cc_start: 0.4448 (t) cc_final: 0.3688 (p) REVERT: I 371 THR cc_start: 0.6843 (p) cc_final: 0.5431 (p) REVERT: K 149 GLN cc_start: 0.9100 (mp10) cc_final: 0.8880 (mp10) REVERT: K 150 ILE cc_start: 0.8253 (mt) cc_final: 0.7774 (mt) REVERT: K 165 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: K 173 GLU cc_start: 0.7513 (mp0) cc_final: 0.7019 (mp0) REVERT: K 186 THR cc_start: 0.5477 (p) cc_final: 0.5232 (p) REVERT: K 188 LYS cc_start: 0.8299 (mtmm) cc_final: 0.7332 (ptpt) REVERT: K 189 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.6336 (m) REVERT: K 190 LEU cc_start: 0.7340 (mt) cc_final: 0.7053 (mt) REVERT: K 204 ILE cc_start: 0.7858 (mt) cc_final: 0.7607 (mt) REVERT: K 207 VAL cc_start: 0.8389 (t) cc_final: 0.7740 (m) REVERT: K 216 ILE cc_start: 0.6021 (OUTLIER) cc_final: 0.5634 (pt) REVERT: K 243 LEU cc_start: 0.8507 (mt) cc_final: 0.7974 (mt) REVERT: K 255 THR cc_start: 0.6484 (OUTLIER) cc_final: 0.6237 (p) REVERT: K 266 MET cc_start: 0.6619 (mtt) cc_final: 0.6417 (mtt) REVERT: K 269 LEU cc_start: 0.8562 (mt) cc_final: 0.8239 (mt) REVERT: K 287 THR cc_start: 0.8333 (t) cc_final: 0.8006 (m) REVERT: K 324 HIS cc_start: 0.7727 (m-70) cc_final: 0.7069 (m-70) REVERT: K 330 LEU cc_start: 0.7005 (pt) cc_final: 0.6417 (pt) REVERT: K 351 ILE cc_start: 0.8522 (mm) cc_final: 0.7718 (mm) REVERT: K 356 THR cc_start: 0.8994 (m) cc_final: 0.8700 (m) REVERT: K 365 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6023 (mt-10) REVERT: K 376 THR cc_start: 0.8236 (p) cc_final: 0.7956 (p) REVERT: L 132 VAL cc_start: 0.6721 (p) cc_final: 0.6469 (p) REVERT: L 140 TYR cc_start: 0.6359 (p90) cc_final: 0.6153 (p90) REVERT: L 161 LEU cc_start: 0.9127 (mt) cc_final: 0.8874 (mm) REVERT: L 202 THR cc_start: 0.7891 (m) cc_final: 0.7180 (p) REVERT: L 260 GLU cc_start: 0.5091 (tt0) cc_final: 0.4611 (tt0) REVERT: L 268 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7347 (pp) REVERT: L 292 ILE cc_start: 0.6423 (tt) cc_final: 0.6181 (tt) REVERT: L 297 ILE cc_start: 0.6505 (tt) cc_final: 0.6078 (tt) REVERT: L 318 ILE cc_start: 0.8065 (mt) cc_final: 0.7395 (tt) REVERT: L 320 ILE cc_start: 0.8108 (mt) cc_final: 0.7861 (mt) REVERT: L 336 PHE cc_start: 0.6836 (m-80) cc_final: 0.6156 (m-80) REVERT: L 364 ARG cc_start: 0.7134 (mtt90) cc_final: 0.6689 (mtt-85) REVERT: M 149 GLN cc_start: 0.8379 (mp10) cc_final: 0.7816 (mp10) REVERT: M 150 ILE cc_start: 0.7462 (mt) cc_final: 0.7108 (mt) REVERT: M 188 LYS cc_start: 0.5654 (mmtp) cc_final: 0.4907 (pttm) REVERT: M 199 THR cc_start: 0.8415 (p) cc_final: 0.7983 (t) REVERT: M 203 PHE cc_start: 0.7633 (t80) cc_final: 0.7023 (t80) REVERT: M 218 GLU cc_start: 0.4206 (OUTLIER) cc_final: 0.3959 (tm-30) REVERT: M 246 ILE cc_start: 0.5909 (tt) cc_final: 0.5206 (tt) REVERT: M 269 LEU cc_start: 0.7967 (mt) cc_final: 0.7732 (mt) REVERT: M 343 THR cc_start: 0.8801 (p) cc_final: 0.8441 (p) REVERT: M 354 ILE cc_start: 0.8507 (mt) cc_final: 0.8231 (tp) REVERT: M 363 ILE cc_start: 0.8518 (mt) cc_final: 0.8315 (mm) REVERT: J 158 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6764 (mt-10) REVERT: J 159 LEU cc_start: 0.7847 (tp) cc_final: 0.7284 (tp) REVERT: J 180 LEU cc_start: 0.7732 (mt) cc_final: 0.7285 (mt) REVERT: J 231 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8074 (mtmp) REVERT: J 272 LEU cc_start: 0.5189 (OUTLIER) cc_final: 0.4405 (tp) REVERT: J 321 PHE cc_start: 0.6740 (m-80) cc_final: 0.6228 (m-80) REVERT: J 324 HIS cc_start: 0.7010 (m170) cc_final: 0.6790 (m-70) REVERT: J 325 THR cc_start: 0.8140 (m) cc_final: 0.7278 (t) REVERT: J 327 LYS cc_start: 0.7672 (tttt) cc_final: 0.7227 (tptt) REVERT: J 339 LEU cc_start: 0.8699 (mt) cc_final: 0.8130 (mt) REVERT: J 364 ARG cc_start: 0.6975 (mtm-85) cc_final: 0.6711 (ptp-110) REVERT: J 374 ASP cc_start: 0.8187 (m-30) cc_final: 0.7355 (m-30) outliers start: 49 outliers final: 10 residues processed: 852 average time/residue: 0.3280 time to fit residues: 365.6286 Evaluate side-chains 646 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 627 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 198 GLN H 252 ASN H 324 HIS I 228 GLN I 267 GLN K 262 GLN L 213 GLN ** L 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN J 198 GLN ** J 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12881 Z= 0.341 Angle : 0.960 15.178 17407 Z= 0.513 Chirality : 0.051 0.260 2000 Planarity : 0.007 0.079 2243 Dihedral : 12.729 131.233 1881 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.86 % Favored : 92.33 % Rotamer: Outliers : 0.75 % Allowed : 4.48 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 2.22 % Twisted General : 0.40 % 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: -1.60 (0.20), residues: 1590 helix: -0.25 (0.17), residues: 786 sheet: -1.19 (0.39), residues: 149 loop : -1.99 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS J 324 PHE 0.038 0.004 PHE H 167 TYR 0.019 0.003 TYR L 140 ARG 0.009 0.001 ARG H 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 752 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 141 GLU cc_start: 0.8932 (pm20) cc_final: 0.8267 (pm20) REVERT: H 186 THR cc_start: 0.7854 (p) cc_final: 0.7503 (p) REVERT: H 241 ASP cc_start: 0.7662 (p0) cc_final: 0.6680 (p0) REVERT: H 255 THR cc_start: 0.3913 (m) cc_final: 0.3396 (m) REVERT: H 268 LEU cc_start: 0.7737 (tp) cc_final: 0.7461 (tp) REVERT: H 269 LEU cc_start: 0.8793 (mt) cc_final: 0.8252 (mt) REVERT: H 320 ILE cc_start: 0.9041 (mt) cc_final: 0.8565 (mt) REVERT: H 324 HIS cc_start: 0.6151 (m90) cc_final: 0.5095 (m90) REVERT: H 363 ILE cc_start: 0.8475 (mt) cc_final: 0.8160 (mt) REVERT: H 372 MET cc_start: 0.7163 (mmm) cc_final: 0.6959 (mmm) REVERT: I 186 THR cc_start: 0.7446 (p) cc_final: 0.6972 (p) REVERT: I 191 LEU cc_start: 0.9238 (tt) cc_final: 0.9021 (tt) REVERT: I 213 GLN cc_start: 0.6942 (pp30) cc_final: 0.6575 (mp10) REVERT: I 268 LEU cc_start: 0.7810 (tp) cc_final: 0.7597 (tp) REVERT: I 289 ARG cc_start: 0.5190 (mtt180) cc_final: 0.4086 (mtm-85) REVERT: I 294 ASP cc_start: 0.8661 (m-30) cc_final: 0.8029 (t0) REVERT: I 318 ILE cc_start: 0.7974 (mt) cc_final: 0.7430 (mt) REVERT: I 319 GLN cc_start: 0.7917 (mm110) cc_final: 0.7680 (mm-40) REVERT: I 325 THR cc_start: 0.8067 (p) cc_final: 0.7413 (p) REVERT: I 326 ARG cc_start: 0.6945 (mtm110) cc_final: 0.6341 (mtm110) REVERT: I 372 MET cc_start: 0.6928 (mmm) cc_final: 0.6448 (mmm) REVERT: K 150 ILE cc_start: 0.8770 (mt) cc_final: 0.8220 (mt) REVERT: K 159 LEU cc_start: 0.7599 (mm) cc_final: 0.7109 (mm) REVERT: K 179 LEU cc_start: 0.7387 (tp) cc_final: 0.6325 (tp) REVERT: K 186 THR cc_start: 0.6047 (p) cc_final: 0.5007 (p) REVERT: K 189 THR cc_start: 0.8085 (m) cc_final: 0.7048 (m) REVERT: K 206 VAL cc_start: 0.8411 (p) cc_final: 0.8110 (p) REVERT: K 207 VAL cc_start: 0.7982 (t) cc_final: 0.7700 (m) REVERT: K 243 LEU cc_start: 0.8727 (mt) cc_final: 0.8113 (mt) REVERT: K 303 PHE cc_start: 0.8051 (m-80) cc_final: 0.7623 (m-80) REVERT: K 320 ILE cc_start: 0.8623 (mt) cc_final: 0.8402 (mt) REVERT: K 325 THR cc_start: 0.8582 (m) cc_final: 0.8360 (m) REVERT: K 351 ILE cc_start: 0.8605 (mm) cc_final: 0.7986 (mm) REVERT: L 132 VAL cc_start: 0.6345 (p) cc_final: 0.5066 (p) REVERT: L 149 GLN cc_start: 0.8464 (mp10) cc_final: 0.7953 (mp10) REVERT: L 153 ILE cc_start: 0.7646 (mt) cc_final: 0.7365 (mt) REVERT: L 154 ARG cc_start: 0.6754 (mmt180) cc_final: 0.6499 (tpp-160) REVERT: L 193 LYS cc_start: 0.7550 (tptt) cc_final: 0.6943 (tptt) REVERT: L 221 ARG cc_start: 0.6847 (tpm170) cc_final: 0.6024 (tpp-160) REVERT: L 225 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7268 (mt-10) REVERT: L 228 GLN cc_start: 0.7992 (tp40) cc_final: 0.7593 (tp40) REVERT: L 231 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8480 (mmtp) REVERT: L 233 LYS cc_start: 0.7585 (tppt) cc_final: 0.7329 (tptp) REVERT: L 238 ILE cc_start: 0.9073 (mt) cc_final: 0.8819 (mp) REVERT: L 284 ILE cc_start: 0.8371 (mm) cc_final: 0.7784 (mm) REVERT: L 320 ILE cc_start: 0.8373 (mt) cc_final: 0.7945 (mm) REVERT: L 328 MET cc_start: 0.7462 (ppp) cc_final: 0.7191 (ppp) REVERT: L 356 THR cc_start: 0.8031 (p) cc_final: 0.7351 (p) REVERT: M 159 LEU cc_start: 0.6673 (tp) cc_final: 0.6465 (tp) REVERT: M 161 LEU cc_start: 0.9028 (mt) cc_final: 0.8798 (mt) REVERT: M 202 THR cc_start: 0.6336 (p) cc_final: 0.5466 (p) REVERT: M 225 GLU cc_start: 0.7844 (pp20) cc_final: 0.7222 (pp20) REVERT: M 228 GLN cc_start: 0.6631 (tp40) cc_final: 0.5156 (tp40) REVERT: M 237 ILE cc_start: 0.6827 (mm) cc_final: 0.6500 (mm) REVERT: M 272 LEU cc_start: 0.6525 (mt) cc_final: 0.6258 (mt) REVERT: M 373 LEU cc_start: 0.8650 (pp) cc_final: 0.8295 (pp) REVERT: M 374 ASP cc_start: 0.6450 (m-30) cc_final: 0.5879 (m-30) REVERT: J 149 GLN cc_start: 0.9400 (mp10) cc_final: 0.8370 (mp10) REVERT: J 159 LEU cc_start: 0.8225 (tp) cc_final: 0.7582 (tp) REVERT: J 184 PRO cc_start: 0.7620 (Cg_exo) cc_final: 0.7405 (Cg_endo) REVERT: J 206 VAL cc_start: 0.8673 (p) cc_final: 0.7834 (p) REVERT: J 214 LYS cc_start: 0.7796 (ptmm) cc_final: 0.6823 (ptmm) REVERT: J 242 GLU cc_start: 0.6228 (tm-30) cc_final: 0.5464 (tm-30) REVERT: J 267 GLN cc_start: 0.8585 (mm110) cc_final: 0.8247 (mm110) REVERT: J 308 GLU cc_start: 0.6069 (pp20) cc_final: 0.5789 (pp20) REVERT: J 313 THR cc_start: 0.7676 (t) cc_final: 0.6948 (t) REVERT: J 324 HIS cc_start: 0.6592 (m170) cc_final: 0.4455 (m-70) REVERT: J 327 LYS cc_start: 0.8372 (tttt) cc_final: 0.8153 (tptt) REVERT: J 343 THR cc_start: 0.9321 (t) cc_final: 0.9054 (t) REVERT: J 351 ILE cc_start: 0.9379 (mt) cc_final: 0.9135 (mt) REVERT: J 366 GLU cc_start: 0.6632 (tp30) cc_final: 0.5388 (tp30) REVERT: J 379 ILE cc_start: 0.9390 (mt) cc_final: 0.8745 (mt) outliers start: 10 outliers final: 4 residues processed: 756 average time/residue: 0.3377 time to fit residues: 336.1739 Evaluate side-chains 594 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 590 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 117 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 126 optimal weight: 0.0770 chunk 140 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 0.0770 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 252 ASN ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 GLN ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.6570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12881 Z= 0.272 Angle : 0.864 14.920 17407 Z= 0.463 Chirality : 0.050 0.288 2000 Planarity : 0.007 0.067 2243 Dihedral : 12.229 130.873 1881 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.98 % Favored : 92.14 % Rotamer: Outliers : 0.37 % Allowed : 5.01 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.20), residues: 1590 helix: -0.40 (0.17), residues: 785 sheet: -1.07 (0.39), residues: 153 loop : -1.57 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS H 324 PHE 0.051 0.003 PHE K 321 TYR 0.024 0.002 TYR I 181 ARG 0.012 0.001 ARG J 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 724 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 186 THR cc_start: 0.7913 (p) cc_final: 0.7671 (p) REVERT: H 221 ARG cc_start: 0.7854 (ppt170) cc_final: 0.7088 (ppt170) REVERT: H 223 VAL cc_start: 0.8901 (t) cc_final: 0.8565 (t) REVERT: H 241 ASP cc_start: 0.7070 (p0) cc_final: 0.6215 (p0) REVERT: H 264 THR cc_start: 0.8573 (p) cc_final: 0.7724 (p) REVERT: H 265 MET cc_start: 0.6440 (tmm) cc_final: 0.6226 (tmm) REVERT: H 267 GLN cc_start: 0.8422 (mt0) cc_final: 0.7899 (mt0) REVERT: H 269 LEU cc_start: 0.8575 (mt) cc_final: 0.8280 (mt) REVERT: H 290 ILE cc_start: 0.7626 (tp) cc_final: 0.7188 (tp) REVERT: H 354 ILE cc_start: 0.8851 (mt) cc_final: 0.8630 (mt) REVERT: H 356 THR cc_start: 0.9030 (p) cc_final: 0.8475 (p) REVERT: H 363 ILE cc_start: 0.8596 (mt) cc_final: 0.8394 (mt) REVERT: H 386 THR cc_start: 0.5352 (p) cc_final: 0.4999 (p) REVERT: I 186 THR cc_start: 0.7784 (p) cc_final: 0.7092 (p) REVERT: I 239 PHE cc_start: 0.6716 (t80) cc_final: 0.6507 (t80) REVERT: I 260 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6841 (mt-10) REVERT: I 294 ASP cc_start: 0.8675 (m-30) cc_final: 0.7991 (m-30) REVERT: I 318 ILE cc_start: 0.8074 (mt) cc_final: 0.7311 (mt) REVERT: I 319 GLN cc_start: 0.7982 (mm110) cc_final: 0.7540 (mm-40) REVERT: I 322 LYS cc_start: 0.9329 (mptt) cc_final: 0.8866 (mmtm) REVERT: I 363 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9140 (mp) REVERT: K 149 GLN cc_start: 0.9258 (mp10) cc_final: 0.8796 (mp10) REVERT: K 189 THR cc_start: 0.7800 (m) cc_final: 0.7392 (p) REVERT: K 207 VAL cc_start: 0.8212 (t) cc_final: 0.7951 (m) REVERT: K 226 VAL cc_start: 0.9072 (t) cc_final: 0.8853 (t) REVERT: K 238 ILE cc_start: 0.7578 (mt) cc_final: 0.7285 (mt) REVERT: K 243 LEU cc_start: 0.8756 (mt) cc_final: 0.8257 (mt) REVERT: K 266 MET cc_start: 0.6559 (mtt) cc_final: 0.5662 (mtt) REVERT: K 267 GLN cc_start: 0.6775 (tp40) cc_final: 0.6185 (tp40) REVERT: K 269 LEU cc_start: 0.8702 (mt) cc_final: 0.8438 (mt) REVERT: K 293 LEU cc_start: 0.8707 (mp) cc_final: 0.8481 (mp) REVERT: K 318 ILE cc_start: 0.7582 (mt) cc_final: 0.7272 (mm) REVERT: K 351 ILE cc_start: 0.8687 (mm) cc_final: 0.8107 (mm) REVERT: K 364 ARG cc_start: 0.7231 (mtm110) cc_final: 0.6547 (mtm110) REVERT: L 149 GLN cc_start: 0.8246 (mp10) cc_final: 0.7913 (mp10) REVERT: L 153 ILE cc_start: 0.7809 (mt) cc_final: 0.7582 (mt) REVERT: L 200 ARG cc_start: 0.6913 (mpp80) cc_final: 0.6683 (mtm180) REVERT: L 210 GLU cc_start: 0.6471 (mm-30) cc_final: 0.6252 (mm-30) REVERT: L 224 ARG cc_start: 0.7265 (ttp-110) cc_final: 0.6769 (ttp-110) REVERT: L 225 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7260 (mt-10) REVERT: L 231 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8660 (mmtm) REVERT: L 238 ILE cc_start: 0.9044 (mt) cc_final: 0.8815 (mp) REVERT: L 284 ILE cc_start: 0.8265 (mm) cc_final: 0.7808 (mm) REVERT: L 317 ARG cc_start: 0.8481 (mmt180) cc_final: 0.8081 (mmt180) REVERT: L 328 MET cc_start: 0.7530 (ppp) cc_final: 0.7157 (ppp) REVERT: L 341 ARG cc_start: 0.8160 (ptp-110) cc_final: 0.7398 (ptp-110) REVERT: L 356 THR cc_start: 0.8091 (p) cc_final: 0.7633 (p) REVERT: L 365 GLU cc_start: 0.4455 (pt0) cc_final: 0.2538 (mt-10) REVERT: L 375 PHE cc_start: 0.6375 (m-80) cc_final: 0.6128 (m-80) REVERT: M 149 GLN cc_start: 0.8623 (mp10) cc_final: 0.8070 (mp10) REVERT: M 152 GLU cc_start: 0.8588 (mp0) cc_final: 0.7281 (mp0) REVERT: M 199 THR cc_start: 0.8458 (p) cc_final: 0.7835 (t) REVERT: M 205 ARG cc_start: 0.6091 (ttt-90) cc_final: 0.5874 (ttt-90) REVERT: M 206 VAL cc_start: 0.7346 (t) cc_final: 0.7123 (t) REVERT: M 210 GLU cc_start: 0.5190 (mt-10) cc_final: 0.4960 (mt-10) REVERT: M 237 ILE cc_start: 0.6626 (mm) cc_final: 0.6355 (mm) REVERT: M 246 ILE cc_start: 0.6106 (tt) cc_final: 0.5862 (tt) REVERT: M 283 VAL cc_start: 0.7956 (m) cc_final: 0.7697 (m) REVERT: M 294 ASP cc_start: 0.6778 (p0) cc_final: 0.6565 (p0) REVERT: M 307 ILE cc_start: 0.6578 (mt) cc_final: 0.6250 (mp) REVERT: M 310 PRO cc_start: 0.8413 (Cg_endo) cc_final: 0.7834 (Cg_exo) REVERT: M 333 ASP cc_start: 0.6834 (p0) cc_final: 0.6218 (p0) REVERT: M 379 ILE cc_start: 0.8306 (pt) cc_final: 0.7989 (pt) REVERT: J 149 GLN cc_start: 0.9357 (mp10) cc_final: 0.8490 (mp10) REVERT: J 159 LEU cc_start: 0.8050 (tp) cc_final: 0.7651 (tp) REVERT: J 199 THR cc_start: 0.8057 (p) cc_final: 0.7621 (p) REVERT: J 214 LYS cc_start: 0.7697 (ptmm) cc_final: 0.6729 (ptmm) REVERT: J 228 GLN cc_start: 0.7792 (mp-120) cc_final: 0.7493 (mt0) REVERT: J 242 GLU cc_start: 0.6351 (tm-30) cc_final: 0.5502 (tm-30) REVERT: J 264 THR cc_start: 0.8013 (m) cc_final: 0.7777 (m) REVERT: J 276 ASP cc_start: 0.6999 (m-30) cc_final: 0.6793 (m-30) REVERT: J 313 THR cc_start: 0.7869 (t) cc_final: 0.7117 (t) REVERT: J 324 HIS cc_start: 0.6335 (m170) cc_final: 0.5426 (m-70) REVERT: J 335 ASP cc_start: 0.6359 (t70) cc_final: 0.5965 (t0) REVERT: J 343 THR cc_start: 0.9177 (t) cc_final: 0.8961 (t) REVERT: J 351 ILE cc_start: 0.9356 (mt) cc_final: 0.9110 (mt) REVERT: J 379 ILE cc_start: 0.9471 (mt) cc_final: 0.9166 (mt) outliers start: 5 outliers final: 0 residues processed: 726 average time/residue: 0.3164 time to fit residues: 302.1531 Evaluate side-chains 581 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 580 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 chunk 150 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 198 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 228 GLN K 262 GLN L 213 GLN ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.7162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12881 Z= 0.271 Angle : 0.840 14.255 17407 Z= 0.448 Chirality : 0.050 0.380 2000 Planarity : 0.006 0.065 2243 Dihedral : 11.828 125.537 1881 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.94 % Allowed : 6.60 % Favored : 92.45 % Rotamer: Outliers : 0.30 % Allowed : 4.33 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.24 (0.21), residues: 1590 helix: -0.28 (0.18), residues: 779 sheet: -0.78 (0.39), residues: 166 loop : -1.39 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.005 HIS L 324 PHE 0.044 0.003 PHE K 361 TYR 0.014 0.002 TYR L 215 ARG 0.008 0.001 ARG I 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 714 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 172 ILE cc_start: 0.7573 (pt) cc_final: 0.7318 (pt) REVERT: H 186 THR cc_start: 0.8162 (p) cc_final: 0.7768 (p) REVERT: H 223 VAL cc_start: 0.9056 (t) cc_final: 0.8658 (t) REVERT: H 265 MET cc_start: 0.6729 (tmm) cc_final: 0.6416 (tmm) REVERT: H 269 LEU cc_start: 0.8661 (mt) cc_final: 0.8265 (mt) REVERT: H 290 ILE cc_start: 0.7723 (tp) cc_final: 0.7134 (tp) REVERT: H 337 LYS cc_start: 0.7857 (mtmt) cc_final: 0.7566 (mtmt) REVERT: H 339 LEU cc_start: 0.8254 (mt) cc_final: 0.8045 (mt) REVERT: H 383 LEU cc_start: 0.8488 (tp) cc_final: 0.8279 (tp) REVERT: I 158 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7555 (pt0) REVERT: I 163 LYS cc_start: 0.7825 (ttmt) cc_final: 0.7567 (ttmm) REVERT: I 186 THR cc_start: 0.7749 (p) cc_final: 0.7526 (p) REVERT: I 260 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6687 (mt-10) REVERT: I 294 ASP cc_start: 0.8311 (m-30) cc_final: 0.7862 (m-30) REVERT: I 318 ILE cc_start: 0.8226 (mt) cc_final: 0.7274 (mt) REVERT: I 325 THR cc_start: 0.7825 (p) cc_final: 0.7571 (p) REVERT: I 351 ILE cc_start: 0.8648 (mt) cc_final: 0.7846 (mt) REVERT: I 355 CYS cc_start: 0.8445 (m) cc_final: 0.7213 (t) REVERT: I 363 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9121 (mp) REVERT: K 149 GLN cc_start: 0.9164 (mp10) cc_final: 0.8873 (mp10) REVERT: K 161 LEU cc_start: 0.8028 (pp) cc_final: 0.6864 (tt) REVERT: K 186 THR cc_start: 0.6606 (p) cc_final: 0.6084 (p) REVERT: K 189 THR cc_start: 0.8363 (m) cc_final: 0.7627 (m) REVERT: K 207 VAL cc_start: 0.8222 (t) cc_final: 0.7927 (m) REVERT: K 211 PHE cc_start: 0.8116 (m-80) cc_final: 0.7679 (m-80) REVERT: K 222 LEU cc_start: 0.8513 (tp) cc_final: 0.8055 (tp) REVERT: K 238 ILE cc_start: 0.7543 (mt) cc_final: 0.7021 (mt) REVERT: K 243 LEU cc_start: 0.8813 (mt) cc_final: 0.8545 (mt) REVERT: K 267 GLN cc_start: 0.6838 (tp40) cc_final: 0.6544 (tp40) REVERT: K 269 LEU cc_start: 0.8868 (mt) cc_final: 0.8537 (mt) REVERT: K 287 THR cc_start: 0.8164 (m) cc_final: 0.7876 (m) REVERT: K 318 ILE cc_start: 0.7732 (mt) cc_final: 0.7355 (mt) REVERT: K 337 LYS cc_start: 0.9267 (pptt) cc_final: 0.8973 (pptt) REVERT: K 351 ILE cc_start: 0.8834 (mm) cc_final: 0.8360 (mm) REVERT: L 153 ILE cc_start: 0.7913 (mt) cc_final: 0.7385 (mt) REVERT: L 154 ARG cc_start: 0.6095 (tpp80) cc_final: 0.5673 (tpp80) REVERT: L 165 GLU cc_start: 0.7788 (pm20) cc_final: 0.7550 (pm20) REVERT: L 193 LYS cc_start: 0.6985 (tptt) cc_final: 0.6750 (tptt) REVERT: L 200 ARG cc_start: 0.7033 (mpp80) cc_final: 0.6726 (mtp180) REVERT: L 206 VAL cc_start: 0.8720 (m) cc_final: 0.8413 (t) REVERT: L 225 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7436 (mt-10) REVERT: L 231 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8502 (mmtp) REVERT: L 238 ILE cc_start: 0.8862 (mt) cc_final: 0.8100 (mt) REVERT: L 284 ILE cc_start: 0.8049 (mm) cc_final: 0.7691 (mm) REVERT: L 317 ARG cc_start: 0.8423 (mmt180) cc_final: 0.7987 (mmt180) REVERT: L 326 ARG cc_start: 0.7918 (pmt-80) cc_final: 0.7579 (pmt-80) REVERT: L 341 ARG cc_start: 0.7851 (ptp-110) cc_final: 0.7055 (ptp-110) REVERT: L 356 THR cc_start: 0.8236 (p) cc_final: 0.7719 (p) REVERT: L 365 GLU cc_start: 0.4355 (pt0) cc_final: 0.2622 (mt-10) REVERT: M 150 ILE cc_start: 0.8015 (mt) cc_final: 0.7799 (mt) REVERT: M 199 THR cc_start: 0.8403 (p) cc_final: 0.8106 (t) REVERT: M 225 GLU cc_start: 0.7762 (pp20) cc_final: 0.7493 (pp20) REVERT: M 246 ILE cc_start: 0.6397 (tt) cc_final: 0.6188 (tt) REVERT: M 266 MET cc_start: 0.6432 (mtt) cc_final: 0.6171 (mtt) REVERT: M 269 LEU cc_start: 0.8029 (mt) cc_final: 0.7638 (mt) REVERT: M 307 ILE cc_start: 0.7019 (mt) cc_final: 0.6709 (mp) REVERT: M 333 ASP cc_start: 0.6632 (p0) cc_final: 0.5984 (p0) REVERT: J 149 GLN cc_start: 0.9223 (mp10) cc_final: 0.8217 (mp10) REVERT: J 188 LYS cc_start: 0.6727 (mttp) cc_final: 0.6141 (mttp) REVERT: J 199 THR cc_start: 0.7736 (p) cc_final: 0.7369 (p) REVERT: J 214 LYS cc_start: 0.7718 (ptmm) cc_final: 0.6795 (ptmm) REVERT: J 223 VAL cc_start: 0.9307 (t) cc_final: 0.6878 (t) REVERT: J 308 GLU cc_start: 0.5944 (pp20) cc_final: 0.5576 (pp20) REVERT: J 313 THR cc_start: 0.8057 (t) cc_final: 0.7181 (t) REVERT: J 335 ASP cc_start: 0.6091 (t70) cc_final: 0.5399 (t0) REVERT: J 356 THR cc_start: 0.8734 (m) cc_final: 0.8451 (m) outliers start: 4 outliers final: 1 residues processed: 714 average time/residue: 0.3098 time to fit residues: 293.1366 Evaluate side-chains 576 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 574 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.0170 chunk 135 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.7864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12881 Z= 0.299 Angle : 0.864 13.555 17407 Z= 0.461 Chirality : 0.051 0.447 2000 Planarity : 0.007 0.144 2243 Dihedral : 11.635 125.150 1881 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 26.93 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.74 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.29 (0.21), residues: 1590 helix: -0.39 (0.18), residues: 780 sheet: -0.41 (0.41), residues: 158 loop : -1.42 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS H 324 PHE 0.062 0.003 PHE K 321 TYR 0.029 0.002 TYR H 140 ARG 0.011 0.001 ARG J 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 688 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 127 VAL cc_start: 0.9331 (m) cc_final: 0.8682 (m) REVERT: H 143 ILE cc_start: 0.7924 (pt) cc_final: 0.7557 (pt) REVERT: H 161 LEU cc_start: 0.8629 (tp) cc_final: 0.8275 (tp) REVERT: H 186 THR cc_start: 0.8428 (p) cc_final: 0.7993 (p) REVERT: H 221 ARG cc_start: 0.7770 (ppt170) cc_final: 0.7360 (ppt170) REVERT: H 239 PHE cc_start: 0.7389 (t80) cc_final: 0.6862 (t80) REVERT: H 264 THR cc_start: 0.8536 (p) cc_final: 0.8123 (p) REVERT: H 269 LEU cc_start: 0.8571 (mt) cc_final: 0.8193 (mt) REVERT: H 290 ILE cc_start: 0.7835 (tp) cc_final: 0.7003 (tp) REVERT: H 323 ILE cc_start: 0.9210 (pt) cc_final: 0.8748 (pt) REVERT: I 186 THR cc_start: 0.8034 (p) cc_final: 0.7717 (p) REVERT: I 224 ARG cc_start: 0.7088 (mtm-85) cc_final: 0.6771 (mpp80) REVERT: I 229 LEU cc_start: 0.8755 (tt) cc_final: 0.8548 (tp) REVERT: I 260 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7431 (mt-10) REVERT: I 282 LYS cc_start: 0.6956 (tptt) cc_final: 0.6753 (tptt) REVERT: I 288 ASN cc_start: 0.8136 (p0) cc_final: 0.7873 (p0) REVERT: I 308 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6505 (tm-30) REVERT: I 310 PRO cc_start: 0.8735 (Cg_endo) cc_final: 0.8243 (Cg_exo) REVERT: I 318 ILE cc_start: 0.8085 (mt) cc_final: 0.7263 (mt) REVERT: I 322 LYS cc_start: 0.9397 (mptt) cc_final: 0.8455 (mmmm) REVERT: I 351 ILE cc_start: 0.8663 (mt) cc_final: 0.8421 (mt) REVERT: I 361 PHE cc_start: 0.7366 (m-80) cc_final: 0.5189 (m-80) REVERT: I 363 ILE cc_start: 0.9407 (mp) cc_final: 0.9146 (mp) REVERT: K 178 VAL cc_start: 0.8636 (t) cc_final: 0.8376 (t) REVERT: K 186 THR cc_start: 0.6805 (p) cc_final: 0.6321 (p) REVERT: K 189 THR cc_start: 0.8753 (m) cc_final: 0.8014 (m) REVERT: K 238 ILE cc_start: 0.7427 (mt) cc_final: 0.6887 (mt) REVERT: K 267 GLN cc_start: 0.7263 (tp40) cc_final: 0.7032 (tp40) REVERT: K 291 ASP cc_start: 0.7525 (m-30) cc_final: 0.7315 (m-30) REVERT: K 310 PRO cc_start: 0.7811 (Cg_endo) cc_final: 0.7423 (Cg_exo) REVERT: K 325 THR cc_start: 0.8713 (m) cc_final: 0.8405 (m) REVERT: K 337 LYS cc_start: 0.9349 (pptt) cc_final: 0.8951 (pptt) REVERT: K 351 ILE cc_start: 0.8773 (mm) cc_final: 0.8339 (mm) REVERT: K 357 GLU cc_start: 0.6681 (tm-30) cc_final: 0.5287 (tm-30) REVERT: L 153 ILE cc_start: 0.8060 (mt) cc_final: 0.7671 (mt) REVERT: L 206 VAL cc_start: 0.8571 (m) cc_final: 0.8342 (t) REVERT: L 223 VAL cc_start: 0.8057 (m) cc_final: 0.7737 (m) REVERT: L 225 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7098 (mt-10) REVERT: L 238 ILE cc_start: 0.8772 (mt) cc_final: 0.8054 (mt) REVERT: L 284 ILE cc_start: 0.8346 (mm) cc_final: 0.7918 (mm) REVERT: L 317 ARG cc_start: 0.8356 (mmt180) cc_final: 0.8022 (mmt180) REVERT: L 337 LYS cc_start: 0.8868 (mppt) cc_final: 0.8541 (mmtm) REVERT: L 341 ARG cc_start: 0.8046 (ptp-110) cc_final: 0.7446 (ptp-110) REVERT: L 356 THR cc_start: 0.8117 (p) cc_final: 0.7775 (p) REVERT: L 372 MET cc_start: 0.5265 (mmm) cc_final: 0.4811 (mmm) REVERT: M 206 VAL cc_start: 0.7094 (t) cc_final: 0.6716 (t) REVERT: M 225 GLU cc_start: 0.7904 (pp20) cc_final: 0.7331 (pp20) REVERT: M 246 ILE cc_start: 0.6356 (tt) cc_final: 0.6081 (tt) REVERT: M 265 MET cc_start: 0.7640 (mtp) cc_final: 0.7269 (mtp) REVERT: M 272 LEU cc_start: 0.6593 (mt) cc_final: 0.6362 (mt) REVERT: M 307 ILE cc_start: 0.7109 (mt) cc_final: 0.6862 (mp) REVERT: M 310 PRO cc_start: 0.8551 (Cg_endo) cc_final: 0.8223 (Cg_exo) REVERT: M 333 ASP cc_start: 0.7037 (p0) cc_final: 0.5988 (p0) REVERT: M 372 MET cc_start: 0.4815 (mmm) cc_final: 0.4432 (mmm) REVERT: J 149 GLN cc_start: 0.9246 (mp10) cc_final: 0.8711 (mp10) REVERT: J 214 LYS cc_start: 0.7130 (ptmm) cc_final: 0.6612 (ptmm) REVERT: J 223 VAL cc_start: 0.9247 (t) cc_final: 0.7298 (t) REVERT: J 264 THR cc_start: 0.8109 (m) cc_final: 0.7870 (m) REVERT: J 343 THR cc_start: 0.9186 (t) cc_final: 0.8880 (t) REVERT: J 356 THR cc_start: 0.8825 (m) cc_final: 0.8570 (m) outliers start: 0 outliers final: 0 residues processed: 688 average time/residue: 0.2963 time to fit residues: 273.6762 Evaluate side-chains 558 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 558 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.0270 chunk 135 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 0.0470 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.8107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12881 Z= 0.262 Angle : 0.841 13.284 17407 Z= 0.447 Chirality : 0.051 0.443 2000 Planarity : 0.006 0.097 2243 Dihedral : 11.548 125.574 1881 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 26.42 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.17 % Favored : 92.08 % Rotamer: Outliers : 0.07 % Allowed : 2.32 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.33 (0.21), residues: 1590 helix: -0.52 (0.17), residues: 782 sheet: -0.18 (0.42), residues: 152 loop : -1.38 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 324 PHE 0.035 0.003 PHE K 361 TYR 0.012 0.002 TYR L 215 ARG 0.015 0.001 ARG K 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 679 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 143 ILE cc_start: 0.7777 (pt) cc_final: 0.7377 (pt) REVERT: H 161 LEU cc_start: 0.8540 (tp) cc_final: 0.8066 (tp) REVERT: H 186 THR cc_start: 0.8475 (p) cc_final: 0.8089 (p) REVERT: H 221 ARG cc_start: 0.7692 (ppt170) cc_final: 0.7491 (ppt170) REVERT: H 239 PHE cc_start: 0.7388 (t80) cc_final: 0.6791 (t80) REVERT: H 269 LEU cc_start: 0.8577 (mt) cc_final: 0.8047 (mt) REVERT: H 363 ILE cc_start: 0.8723 (mt) cc_final: 0.8467 (mt) REVERT: H 366 GLU cc_start: 0.7481 (mp0) cc_final: 0.7251 (mp0) REVERT: H 386 THR cc_start: 0.5305 (p) cc_final: 0.5051 (p) REVERT: I 221 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7092 (ttp80) REVERT: I 308 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6589 (tm-30) REVERT: I 315 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6618 (tm-30) REVERT: I 318 ILE cc_start: 0.8424 (mt) cc_final: 0.7486 (mt) REVERT: I 322 LYS cc_start: 0.9325 (mptt) cc_final: 0.8413 (mmmm) REVERT: I 323 ILE cc_start: 0.9141 (mm) cc_final: 0.8001 (mm) REVERT: I 326 ARG cc_start: 0.7016 (mtm110) cc_final: 0.5391 (ptp90) REVERT: I 351 ILE cc_start: 0.8616 (mt) cc_final: 0.8236 (mt) REVERT: I 363 ILE cc_start: 0.9343 (mp) cc_final: 0.9001 (mp) REVERT: K 161 LEU cc_start: 0.7919 (pp) cc_final: 0.7385 (tt) REVERT: K 186 THR cc_start: 0.6712 (p) cc_final: 0.6151 (p) REVERT: K 189 THR cc_start: 0.8832 (m) cc_final: 0.8098 (m) REVERT: K 238 ILE cc_start: 0.7372 (mt) cc_final: 0.7023 (mt) REVERT: K 262 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6135 (mt0) REVERT: K 267 GLN cc_start: 0.7219 (tp40) cc_final: 0.6673 (tp40) REVERT: K 269 LEU cc_start: 0.8894 (mt) cc_final: 0.8641 (mt) REVERT: K 310 PRO cc_start: 0.7658 (Cg_endo) cc_final: 0.7262 (Cg_exo) REVERT: K 318 ILE cc_start: 0.7143 (mm) cc_final: 0.6861 (mm) REVERT: K 325 THR cc_start: 0.8748 (m) cc_final: 0.8398 (m) REVERT: K 337 LYS cc_start: 0.9411 (pptt) cc_final: 0.9006 (pptt) REVERT: K 351 ILE cc_start: 0.8724 (mm) cc_final: 0.8388 (mm) REVERT: L 132 VAL cc_start: 0.5770 (p) cc_final: 0.4955 (p) REVERT: L 137 GLU cc_start: 0.8263 (pm20) cc_final: 0.8047 (pm20) REVERT: L 153 ILE cc_start: 0.8105 (mt) cc_final: 0.7665 (mt) REVERT: L 205 ARG cc_start: 0.6617 (ttp80) cc_final: 0.6226 (ttp-110) REVERT: L 206 VAL cc_start: 0.8650 (m) cc_final: 0.8277 (t) REVERT: L 222 LEU cc_start: 0.8313 (mt) cc_final: 0.7929 (mt) REVERT: L 225 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7835 (mt-10) REVERT: L 238 ILE cc_start: 0.8727 (mt) cc_final: 0.7982 (mt) REVERT: L 284 ILE cc_start: 0.8099 (mm) cc_final: 0.7754 (mm) REVERT: L 356 THR cc_start: 0.8315 (p) cc_final: 0.7863 (p) REVERT: L 365 GLU cc_start: 0.4453 (pt0) cc_final: 0.2712 (mt-10) REVERT: L 375 PHE cc_start: 0.6314 (m-80) cc_final: 0.6052 (m-80) REVERT: M 225 GLU cc_start: 0.7759 (pp20) cc_final: 0.7279 (pp20) REVERT: M 246 ILE cc_start: 0.6660 (tt) cc_final: 0.6281 (tt) REVERT: M 264 THR cc_start: 0.8595 (p) cc_final: 0.8146 (p) REVERT: M 283 VAL cc_start: 0.8025 (m) cc_final: 0.7778 (m) REVERT: M 310 PRO cc_start: 0.8481 (Cg_endo) cc_final: 0.8193 (Cg_exo) REVERT: M 333 ASP cc_start: 0.6885 (p0) cc_final: 0.5626 (p0) REVERT: M 372 MET cc_start: 0.4385 (mmm) cc_final: 0.4014 (mmm) REVERT: J 214 LYS cc_start: 0.6970 (ptmm) cc_final: 0.6349 (ptmm) REVERT: J 223 VAL cc_start: 0.9207 (t) cc_final: 0.7166 (t) REVERT: J 264 THR cc_start: 0.8108 (m) cc_final: 0.7766 (m) REVERT: J 374 ASP cc_start: 0.8596 (m-30) cc_final: 0.8248 (m-30) REVERT: J 383 LEU cc_start: 0.8850 (mm) cc_final: 0.8548 (mm) outliers start: 1 outliers final: 0 residues processed: 680 average time/residue: 0.3049 time to fit residues: 276.6694 Evaluate side-chains 577 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 576 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 150 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN J 197 ASN ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.8493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12881 Z= 0.298 Angle : 0.872 13.245 17407 Z= 0.463 Chirality : 0.051 0.419 2000 Planarity : 0.007 0.124 2243 Dihedral : 11.522 125.766 1881 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 28.25 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.86 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.39 (0.21), residues: 1590 helix: -0.61 (0.18), residues: 773 sheet: -0.24 (0.41), residues: 160 loop : -1.34 (0.26), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 324 PHE 0.034 0.003 PHE K 361 TYR 0.032 0.002 TYR H 140 ARG 0.015 0.001 ARG K 263 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 667 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 143 ILE cc_start: 0.7992 (pt) cc_final: 0.7660 (pt) REVERT: H 161 LEU cc_start: 0.8530 (tp) cc_final: 0.8202 (tp) REVERT: H 186 THR cc_start: 0.8575 (p) cc_final: 0.8101 (p) REVERT: H 221 ARG cc_start: 0.7960 (ppt170) cc_final: 0.7625 (ppt170) REVERT: H 239 PHE cc_start: 0.7419 (t80) cc_final: 0.6810 (t80) REVERT: H 269 LEU cc_start: 0.8578 (mt) cc_final: 0.8097 (mt) REVERT: H 276 ASP cc_start: 0.7765 (m-30) cc_final: 0.7409 (m-30) REVERT: H 290 ILE cc_start: 0.7615 (tp) cc_final: 0.6939 (tp) REVERT: H 323 ILE cc_start: 0.8911 (pt) cc_final: 0.8710 (pt) REVERT: H 363 ILE cc_start: 0.8688 (mt) cc_final: 0.8336 (mt) REVERT: H 373 LEU cc_start: 0.8461 (tp) cc_final: 0.8255 (tt) REVERT: H 386 THR cc_start: 0.5561 (p) cc_final: 0.5314 (p) REVERT: I 221 ARG cc_start: 0.7578 (ttp80) cc_final: 0.6951 (ttp80) REVERT: I 260 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7237 (mt-10) REVERT: I 308 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6078 (tm-30) REVERT: I 309 VAL cc_start: 0.9076 (p) cc_final: 0.8710 (p) REVERT: I 310 PRO cc_start: 0.8306 (Cg_endo) cc_final: 0.7500 (Cg_exo) REVERT: I 318 ILE cc_start: 0.8507 (mt) cc_final: 0.7474 (mt) REVERT: I 322 LYS cc_start: 0.9369 (mptt) cc_final: 0.8558 (mmmm) REVERT: I 351 ILE cc_start: 0.8584 (mt) cc_final: 0.8173 (mt) REVERT: I 356 THR cc_start: 0.9578 (m) cc_final: 0.9065 (p) REVERT: K 149 GLN cc_start: 0.9111 (mp10) cc_final: 0.8876 (mp10) REVERT: K 172 ILE cc_start: 0.5155 (tp) cc_final: 0.4908 (tp) REVERT: K 186 THR cc_start: 0.6976 (p) cc_final: 0.6297 (p) REVERT: K 189 THR cc_start: 0.9008 (m) cc_final: 0.8343 (m) REVERT: K 211 PHE cc_start: 0.8218 (m-80) cc_final: 0.7957 (m-80) REVERT: K 238 ILE cc_start: 0.7490 (mt) cc_final: 0.6858 (mt) REVERT: K 267 GLN cc_start: 0.7197 (tp40) cc_final: 0.6809 (tp40) REVERT: K 318 ILE cc_start: 0.7147 (mm) cc_final: 0.6930 (mm) REVERT: K 325 THR cc_start: 0.8772 (m) cc_final: 0.8373 (m) REVERT: K 337 LYS cc_start: 0.9370 (pptt) cc_final: 0.8931 (pptt) REVERT: K 351 ILE cc_start: 0.8733 (mm) cc_final: 0.8434 (mm) REVERT: K 372 MET cc_start: 0.6015 (mmm) cc_final: 0.5208 (mmm) REVERT: L 132 VAL cc_start: 0.6424 (p) cc_final: 0.5149 (p) REVERT: L 153 ILE cc_start: 0.8003 (mt) cc_final: 0.7775 (mt) REVERT: L 203 PHE cc_start: 0.6584 (t80) cc_final: 0.6308 (t80) REVERT: L 205 ARG cc_start: 0.6266 (ttp80) cc_final: 0.5927 (ttp80) REVERT: L 221 ARG cc_start: 0.6688 (tpm170) cc_final: 0.6122 (tpm170) REVERT: L 222 LEU cc_start: 0.8200 (mt) cc_final: 0.7911 (mt) REVERT: L 225 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7562 (mt-10) REVERT: L 233 LYS cc_start: 0.8482 (tppt) cc_final: 0.8262 (tptm) REVERT: L 238 ILE cc_start: 0.8689 (mt) cc_final: 0.8037 (mt) REVERT: L 284 ILE cc_start: 0.8487 (mm) cc_final: 0.7718 (mm) REVERT: L 356 THR cc_start: 0.8268 (p) cc_final: 0.7782 (p) REVERT: L 365 GLU cc_start: 0.4747 (pt0) cc_final: 0.2856 (mt-10) REVERT: M 150 ILE cc_start: 0.8575 (mt) cc_final: 0.8303 (mt) REVERT: M 154 ARG cc_start: 0.6920 (ptt180) cc_final: 0.6541 (ptt180) REVERT: M 206 VAL cc_start: 0.7052 (t) cc_final: 0.6789 (t) REVERT: M 225 GLU cc_start: 0.7814 (pp20) cc_final: 0.7343 (pp20) REVERT: M 229 LEU cc_start: 0.8693 (mt) cc_final: 0.8017 (mt) REVERT: M 246 ILE cc_start: 0.6431 (tt) cc_final: 0.6230 (tt) REVERT: M 272 LEU cc_start: 0.6252 (mt) cc_final: 0.5851 (mt) REVERT: M 283 VAL cc_start: 0.8132 (m) cc_final: 0.7905 (m) REVERT: M 307 ILE cc_start: 0.6680 (mp) cc_final: 0.6241 (mt) REVERT: M 310 PRO cc_start: 0.8605 (Cg_endo) cc_final: 0.8264 (Cg_exo) REVERT: M 333 ASP cc_start: 0.6471 (p0) cc_final: 0.5186 (p0) REVERT: M 374 ASP cc_start: 0.6971 (m-30) cc_final: 0.5806 (m-30) REVERT: M 382 VAL cc_start: 0.7649 (t) cc_final: 0.7160 (t) REVERT: J 149 GLN cc_start: 0.9479 (mp10) cc_final: 0.8536 (mp10) REVERT: J 167 PHE cc_start: 0.6438 (m-80) cc_final: 0.6140 (m-80) REVERT: J 214 LYS cc_start: 0.7800 (ptmm) cc_final: 0.7522 (ptmm) REVERT: J 223 VAL cc_start: 0.9148 (t) cc_final: 0.6555 (t) REVERT: J 327 LYS cc_start: 0.8179 (tmtt) cc_final: 0.7356 (tptt) REVERT: J 354 ILE cc_start: 0.8903 (tt) cc_final: 0.7911 (tt) REVERT: J 356 THR cc_start: 0.9056 (m) cc_final: 0.8657 (m) REVERT: J 361 PHE cc_start: 0.8012 (m-10) cc_final: 0.7299 (m-80) REVERT: J 379 ILE cc_start: 0.9616 (mt) cc_final: 0.9271 (mt) REVERT: J 383 LEU cc_start: 0.8689 (mm) cc_final: 0.8342 (mm) outliers start: 0 outliers final: 0 residues processed: 667 average time/residue: 0.3087 time to fit residues: 278.2321 Evaluate side-chains 577 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 577 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 144 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 ASN ** L 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN J 197 ASN ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.8712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12881 Z= 0.278 Angle : 0.877 16.473 17407 Z= 0.465 Chirality : 0.051 0.430 2000 Planarity : 0.006 0.105 2243 Dihedral : 11.414 126.287 1881 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 28.06 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.67 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.41 (0.21), residues: 1590 helix: -0.67 (0.18), residues: 772 sheet: -0.22 (0.43), residues: 152 loop : -1.29 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 324 PHE 0.067 0.003 PHE M 321 TYR 0.029 0.002 TYR M 215 ARG 0.014 0.001 ARG K 305 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 668 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 143 ILE cc_start: 0.8025 (pt) cc_final: 0.7475 (pt) REVERT: H 161 LEU cc_start: 0.8250 (tp) cc_final: 0.7884 (tp) REVERT: H 239 PHE cc_start: 0.7414 (t80) cc_final: 0.6953 (t80) REVERT: H 269 LEU cc_start: 0.8656 (mt) cc_final: 0.8052 (mt) REVERT: H 276 ASP cc_start: 0.8023 (m-30) cc_final: 0.7747 (m-30) REVERT: H 290 ILE cc_start: 0.7547 (tp) cc_final: 0.6859 (tp) REVERT: H 323 ILE cc_start: 0.8797 (pt) cc_final: 0.7664 (pt) REVERT: H 363 ILE cc_start: 0.8705 (mt) cc_final: 0.8285 (mt) REVERT: H 373 LEU cc_start: 0.8308 (tp) cc_final: 0.7781 (tt) REVERT: H 374 ASP cc_start: 0.7840 (m-30) cc_final: 0.7087 (m-30) REVERT: H 386 THR cc_start: 0.5639 (p) cc_final: 0.5352 (p) REVERT: I 221 ARG cc_start: 0.7485 (ttp80) cc_final: 0.6957 (ttp80) REVERT: I 308 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6539 (tm-30) REVERT: I 315 GLU cc_start: 0.6930 (tm-30) cc_final: 0.6625 (tm-30) REVERT: I 318 ILE cc_start: 0.8494 (mt) cc_final: 0.7577 (mt) REVERT: I 322 LYS cc_start: 0.9332 (mptt) cc_final: 0.8509 (mmmm) REVERT: I 356 THR cc_start: 0.9538 (m) cc_final: 0.8918 (p) REVERT: K 148 VAL cc_start: 0.9122 (p) cc_final: 0.8727 (p) REVERT: K 149 GLN cc_start: 0.8989 (mp10) cc_final: 0.8592 (mp10) REVERT: K 151 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7558 (mt-10) REVERT: K 152 GLU cc_start: 0.7822 (pm20) cc_final: 0.7575 (mp0) REVERT: K 186 THR cc_start: 0.7269 (p) cc_final: 0.6594 (p) REVERT: K 189 THR cc_start: 0.8983 (m) cc_final: 0.8438 (m) REVERT: K 206 VAL cc_start: 0.8712 (t) cc_final: 0.8472 (t) REVERT: K 211 PHE cc_start: 0.8141 (m-80) cc_final: 0.7890 (m-80) REVERT: K 222 LEU cc_start: 0.8490 (tp) cc_final: 0.8290 (tp) REVERT: K 238 ILE cc_start: 0.7526 (mt) cc_final: 0.7136 (mt) REVERT: K 260 GLU cc_start: 0.6017 (tp30) cc_final: 0.5604 (tp30) REVERT: K 318 ILE cc_start: 0.7237 (mm) cc_final: 0.6970 (mm) REVERT: K 325 THR cc_start: 0.8730 (m) cc_final: 0.8330 (m) REVERT: K 337 LYS cc_start: 0.9328 (pptt) cc_final: 0.8910 (pptt) REVERT: K 351 ILE cc_start: 0.8706 (mm) cc_final: 0.8440 (mm) REVERT: K 357 GLU cc_start: 0.6955 (tm-30) cc_final: 0.5369 (tm-30) REVERT: K 372 MET cc_start: 0.6187 (mmm) cc_final: 0.5208 (mmm) REVERT: K 374 ASP cc_start: 0.7441 (m-30) cc_final: 0.7171 (m-30) REVERT: K 377 LYS cc_start: 0.8936 (ptpt) cc_final: 0.8579 (pttm) REVERT: L 132 VAL cc_start: 0.6856 (p) cc_final: 0.5742 (p) REVERT: L 153 ILE cc_start: 0.8293 (mt) cc_final: 0.7948 (mt) REVERT: L 193 LYS cc_start: 0.6897 (tptt) cc_final: 0.6680 (tptt) REVERT: L 221 ARG cc_start: 0.6516 (tpm170) cc_final: 0.6035 (tpm170) REVERT: L 225 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7485 (mt-10) REVERT: L 238 ILE cc_start: 0.8471 (mt) cc_final: 0.7958 (mt) REVERT: L 240 ILE cc_start: 0.8287 (tp) cc_final: 0.8027 (tp) REVERT: L 284 ILE cc_start: 0.8196 (mm) cc_final: 0.7624 (mm) REVERT: L 356 THR cc_start: 0.8250 (p) cc_final: 0.7738 (p) REVERT: L 365 GLU cc_start: 0.4723 (pt0) cc_final: 0.2783 (mt-10) REVERT: M 199 THR cc_start: 0.8233 (p) cc_final: 0.7896 (t) REVERT: M 225 GLU cc_start: 0.7880 (pp20) cc_final: 0.7480 (pp20) REVERT: M 229 LEU cc_start: 0.8656 (mt) cc_final: 0.8035 (mt) REVERT: M 272 LEU cc_start: 0.6229 (mt) cc_final: 0.5662 (mt) REVERT: M 283 VAL cc_start: 0.8168 (m) cc_final: 0.7915 (m) REVERT: M 310 PRO cc_start: 0.8538 (Cg_endo) cc_final: 0.8115 (Cg_exo) REVERT: M 333 ASP cc_start: 0.5628 (p0) cc_final: 0.4770 (p0) REVERT: J 149 GLN cc_start: 0.9274 (mp10) cc_final: 0.8634 (mp10) REVERT: J 223 VAL cc_start: 0.9071 (t) cc_final: 0.6899 (t) REVERT: J 327 LYS cc_start: 0.8070 (tmtt) cc_final: 0.7474 (tptt) REVERT: J 343 THR cc_start: 0.9045 (t) cc_final: 0.8735 (t) REVERT: J 354 ILE cc_start: 0.8690 (tt) cc_final: 0.8395 (tt) REVERT: J 356 THR cc_start: 0.9171 (m) cc_final: 0.8778 (m) REVERT: J 361 PHE cc_start: 0.7234 (m-10) cc_final: 0.6952 (m-10) REVERT: J 379 ILE cc_start: 0.9332 (mt) cc_final: 0.9043 (mt) REVERT: J 383 LEU cc_start: 0.8824 (mm) cc_final: 0.8470 (mm) outliers start: 0 outliers final: 0 residues processed: 668 average time/residue: 0.3080 time to fit residues: 278.7738 Evaluate side-chains 578 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 578 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0570 chunk 140 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 110 optimal weight: 0.0670 chunk 42 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 132 optimal weight: 0.4980 chunk 139 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN J 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.8854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12881 Z= 0.266 Angle : 0.906 14.890 17407 Z= 0.476 Chirality : 0.053 0.465 2000 Planarity : 0.007 0.094 2243 Dihedral : 11.209 125.676 1881 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 26.93 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.80 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.36 (0.21), residues: 1590 helix: -0.65 (0.18), residues: 782 sheet: -0.16 (0.43), residues: 152 loop : -1.24 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS K 324 PHE 0.058 0.003 PHE K 361 TYR 0.029 0.002 TYR K 140 ARG 0.028 0.001 ARG L 263 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 649 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 143 ILE cc_start: 0.7792 (pt) cc_final: 0.7404 (pt) REVERT: H 161 LEU cc_start: 0.8196 (tp) cc_final: 0.7913 (tp) REVERT: H 239 PHE cc_start: 0.7400 (t80) cc_final: 0.6999 (t80) REVERT: H 269 LEU cc_start: 0.8650 (mt) cc_final: 0.8127 (mt) REVERT: H 276 ASP cc_start: 0.7840 (m-30) cc_final: 0.7540 (m-30) REVERT: H 290 ILE cc_start: 0.7389 (tp) cc_final: 0.6738 (tp) REVERT: H 363 ILE cc_start: 0.8681 (mt) cc_final: 0.8384 (mt) REVERT: H 373 LEU cc_start: 0.8112 (tp) cc_final: 0.7691 (tt) REVERT: H 376 THR cc_start: 0.8473 (p) cc_final: 0.8207 (p) REVERT: I 140 TYR cc_start: 0.6320 (m-10) cc_final: 0.5992 (m-10) REVERT: I 221 ARG cc_start: 0.7390 (ttp80) cc_final: 0.6925 (ttp80) REVERT: I 284 ILE cc_start: 0.9095 (mt) cc_final: 0.8826 (mt) REVERT: I 308 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6480 (tm-30) REVERT: I 318 ILE cc_start: 0.8674 (mt) cc_final: 0.7623 (mt) REVERT: I 322 LYS cc_start: 0.9304 (mptt) cc_final: 0.8475 (mmmm) REVERT: I 342 ILE cc_start: 0.9077 (mt) cc_final: 0.8870 (mt) REVERT: I 356 THR cc_start: 0.9499 (m) cc_final: 0.9125 (p) REVERT: K 148 VAL cc_start: 0.9126 (p) cc_final: 0.8807 (p) REVERT: K 151 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7212 (tp30) REVERT: K 154 ARG cc_start: 0.7082 (ttp80) cc_final: 0.6771 (ttp80) REVERT: K 186 THR cc_start: 0.7101 (p) cc_final: 0.6248 (p) REVERT: K 189 THR cc_start: 0.9026 (m) cc_final: 0.8485 (m) REVERT: K 211 PHE cc_start: 0.8161 (m-80) cc_final: 0.7700 (m-80) REVERT: K 222 LEU cc_start: 0.8587 (tp) cc_final: 0.8387 (tp) REVERT: K 238 ILE cc_start: 0.7487 (mt) cc_final: 0.7261 (mt) REVERT: K 263 ARG cc_start: 0.7032 (mpp-170) cc_final: 0.6771 (mpp-170) REVERT: K 315 GLU cc_start: 0.8289 (pm20) cc_final: 0.7965 (pm20) REVERT: K 318 ILE cc_start: 0.7263 (mm) cc_final: 0.6988 (mm) REVERT: K 325 THR cc_start: 0.8697 (m) cc_final: 0.8229 (m) REVERT: K 337 LYS cc_start: 0.9324 (pptt) cc_final: 0.8930 (pptt) REVERT: K 351 ILE cc_start: 0.8659 (mm) cc_final: 0.8382 (mm) REVERT: K 360 MET cc_start: 0.7224 (ppp) cc_final: 0.7023 (ppp) REVERT: K 361 PHE cc_start: 0.6821 (m-80) cc_final: 0.6484 (m-80) REVERT: K 372 MET cc_start: 0.6053 (mmm) cc_final: 0.5169 (mmm) REVERT: L 153 ILE cc_start: 0.8234 (mt) cc_final: 0.8011 (mt) REVERT: L 221 ARG cc_start: 0.6537 (tpm170) cc_final: 0.5762 (tpm170) REVERT: L 222 LEU cc_start: 0.8177 (mt) cc_final: 0.7750 (mt) REVERT: L 225 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7642 (mt-10) REVERT: L 238 ILE cc_start: 0.8493 (mt) cc_final: 0.7961 (mt) REVERT: L 240 ILE cc_start: 0.8350 (tp) cc_final: 0.7821 (tp) REVERT: L 284 ILE cc_start: 0.8177 (mm) cc_final: 0.7401 (mm) REVERT: L 320 ILE cc_start: 0.8208 (tp) cc_final: 0.7690 (mm) REVERT: L 356 THR cc_start: 0.8080 (p) cc_final: 0.7235 (p) REVERT: L 365 GLU cc_start: 0.4923 (pt0) cc_final: 0.2885 (mt-10) REVERT: M 199 THR cc_start: 0.8112 (p) cc_final: 0.7813 (t) REVERT: M 225 GLU cc_start: 0.7920 (pp20) cc_final: 0.7522 (pp20) REVERT: M 229 LEU cc_start: 0.8618 (mt) cc_final: 0.7743 (mt) REVERT: M 272 LEU cc_start: 0.5819 (mt) cc_final: 0.5524 (mt) REVERT: M 283 VAL cc_start: 0.8155 (m) cc_final: 0.7924 (m) REVERT: M 333 ASP cc_start: 0.5745 (p0) cc_final: 0.5221 (p0) REVERT: M 370 VAL cc_start: 0.6285 (t) cc_final: 0.5912 (t) REVERT: M 382 VAL cc_start: 0.8166 (t) cc_final: 0.6915 (t) REVERT: J 149 GLN cc_start: 0.9353 (mp10) cc_final: 0.8472 (mp10) REVERT: J 223 VAL cc_start: 0.9045 (t) cc_final: 0.6818 (t) REVERT: J 327 LYS cc_start: 0.7913 (tmtt) cc_final: 0.7433 (tptt) REVERT: J 343 THR cc_start: 0.8993 (t) cc_final: 0.8769 (t) REVERT: J 354 ILE cc_start: 0.8634 (tt) cc_final: 0.8394 (tt) REVERT: J 356 THR cc_start: 0.9208 (m) cc_final: 0.8682 (m) REVERT: J 379 ILE cc_start: 0.9385 (mt) cc_final: 0.9158 (mt) outliers start: 0 outliers final: 0 residues processed: 649 average time/residue: 0.3043 time to fit residues: 266.7968 Evaluate side-chains 563 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 563 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 143 optimal weight: 0.4980 chunk 123 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 0.0060 chunk 75 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN J 197 ASN J 262 GLN ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.9092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12881 Z= 0.289 Angle : 0.904 12.305 17407 Z= 0.478 Chirality : 0.052 0.434 2000 Planarity : 0.007 0.105 2243 Dihedral : 11.053 125.228 1881 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 30.35 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.67 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % 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: -1.42 (0.21), residues: 1590 helix: -0.69 (0.18), residues: 774 sheet: -0.31 (0.41), residues: 159 loop : -1.26 (0.26), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.003 HIS H 324 PHE 0.053 0.003 PHE M 321 TYR 0.015 0.002 TYR L 215 ARG 0.016 0.001 ARG H 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 640 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 143 ILE cc_start: 0.8173 (pt) cc_final: 0.7738 (pt) REVERT: H 161 LEU cc_start: 0.8145 (tp) cc_final: 0.7867 (tp) REVERT: H 239 PHE cc_start: 0.7523 (t80) cc_final: 0.7050 (t80) REVERT: H 269 LEU cc_start: 0.8722 (mt) cc_final: 0.8184 (mt) REVERT: H 276 ASP cc_start: 0.7811 (m-30) cc_final: 0.7551 (m-30) REVERT: H 290 ILE cc_start: 0.7711 (tp) cc_final: 0.6889 (tp) REVERT: H 360 MET cc_start: 0.5976 (ptt) cc_final: 0.5115 (ptt) REVERT: H 376 THR cc_start: 0.8583 (p) cc_final: 0.8187 (p) REVERT: I 198 GLN cc_start: 0.8151 (mp-120) cc_final: 0.7442 (mm-40) REVERT: I 216 ILE cc_start: 0.7466 (pt) cc_final: 0.7042 (pt) REVERT: I 221 ARG cc_start: 0.7424 (ttp80) cc_final: 0.6911 (ttp80) REVERT: I 231 LYS cc_start: 0.8661 (mmmt) cc_final: 0.8422 (mmmt) REVERT: I 284 ILE cc_start: 0.9173 (mt) cc_final: 0.8873 (mt) REVERT: I 309 VAL cc_start: 0.9010 (p) cc_final: 0.8713 (p) REVERT: I 318 ILE cc_start: 0.8512 (mt) cc_final: 0.7584 (mt) REVERT: I 322 LYS cc_start: 0.9317 (mptt) cc_final: 0.8544 (mmmm) REVERT: I 356 THR cc_start: 0.9661 (m) cc_final: 0.9112 (p) REVERT: K 148 VAL cc_start: 0.9216 (p) cc_final: 0.8843 (p) REVERT: K 151 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7243 (tp30) REVERT: K 170 VAL cc_start: 0.5028 (m) cc_final: 0.4786 (m) REVERT: K 186 THR cc_start: 0.7178 (p) cc_final: 0.6502 (p) REVERT: K 238 ILE cc_start: 0.7604 (mt) cc_final: 0.7239 (mt) REVERT: K 310 PRO cc_start: 0.8301 (Cg_endo) cc_final: 0.8067 (Cg_exo) REVERT: K 337 LYS cc_start: 0.9379 (pptt) cc_final: 0.8935 (pptt) REVERT: K 338 GLU cc_start: 0.6949 (tp30) cc_final: 0.6444 (tp30) REVERT: K 361 PHE cc_start: 0.6907 (m-80) cc_final: 0.6530 (m-80) REVERT: K 372 MET cc_start: 0.6291 (mmm) cc_final: 0.5351 (mmm) REVERT: L 193 LYS cc_start: 0.6889 (tptt) cc_final: 0.5947 (mmmt) REVERT: L 221 ARG cc_start: 0.6761 (tpm170) cc_final: 0.6122 (tpm170) REVERT: L 222 LEU cc_start: 0.8084 (mt) cc_final: 0.7821 (mt) REVERT: L 225 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7675 (mt-10) REVERT: L 238 ILE cc_start: 0.8434 (mt) cc_final: 0.7905 (mt) REVERT: L 240 ILE cc_start: 0.8323 (tp) cc_final: 0.7910 (tp) REVERT: L 284 ILE cc_start: 0.8099 (mm) cc_final: 0.7606 (mm) REVERT: L 356 THR cc_start: 0.8064 (p) cc_final: 0.7220 (p) REVERT: L 365 GLU cc_start: 0.4924 (pt0) cc_final: 0.2755 (mt-10) REVERT: M 179 LEU cc_start: 0.7889 (tp) cc_final: 0.7476 (tp) REVERT: M 199 THR cc_start: 0.8222 (p) cc_final: 0.7977 (t) REVERT: M 225 GLU cc_start: 0.7974 (pp20) cc_final: 0.7611 (pp20) REVERT: M 229 LEU cc_start: 0.8602 (mt) cc_final: 0.7988 (mt) REVERT: M 272 LEU cc_start: 0.5976 (mt) cc_final: 0.5467 (mt) REVERT: M 294 ASP cc_start: 0.6450 (p0) cc_final: 0.6211 (p0) REVERT: M 307 ILE cc_start: 0.6829 (mp) cc_final: 0.6291 (mp) REVERT: M 328 MET cc_start: 0.6582 (tmm) cc_final: 0.6201 (tmm) REVERT: M 333 ASP cc_start: 0.5908 (p0) cc_final: 0.5555 (p0) REVERT: M 382 VAL cc_start: 0.8282 (t) cc_final: 0.7008 (t) REVERT: J 149 GLN cc_start: 0.9363 (mp10) cc_final: 0.8891 (mp10) REVERT: J 223 VAL cc_start: 0.9067 (t) cc_final: 0.7153 (t) REVERT: J 224 ARG cc_start: 0.7752 (ptp-110) cc_final: 0.6593 (ptp-170) REVERT: J 327 LYS cc_start: 0.8027 (tmtt) cc_final: 0.7630 (tptt) REVERT: J 343 THR cc_start: 0.9034 (t) cc_final: 0.8804 (t) REVERT: J 356 THR cc_start: 0.9117 (m) cc_final: 0.8684 (m) REVERT: J 379 ILE cc_start: 0.9442 (mt) cc_final: 0.9150 (mt) outliers start: 0 outliers final: 0 residues processed: 640 average time/residue: 0.2947 time to fit residues: 253.5639 Evaluate side-chains 546 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 546 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 108 optimal weight: 3.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN J 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.132119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.105398 restraints weight = 34468.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.109023 restraints weight = 25599.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.111913 restraints weight = 19878.359| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.9292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12881 Z= 0.269 Angle : 0.895 11.895 17407 Z= 0.474 Chirality : 0.052 0.460 2000 Planarity : 0.007 0.106 2243 Dihedral : 10.911 126.498 1881 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 28.99 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.24 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % 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: -1.36 (0.21), residues: 1590 helix: -0.64 (0.18), residues: 771 sheet: -0.24 (0.41), residues: 151 loop : -1.22 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS K 324 PHE 0.040 0.003 PHE K 361 TYR 0.019 0.002 TYR M 181 ARG 0.019 0.001 ARG H 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4822.68 seconds wall clock time: 85 minutes 54.69 seconds (5154.69 seconds total)