Starting phenix.real_space_refine (version: dev) on Mon Dec 12 23:15:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/12_2022/6he4_0209_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/12_2022/6he4_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_0209/12_2022/6he4_0209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/12_2022/6he4_0209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/12_2022/6he4_0209_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/12_2022/6he4_0209_updated.pdb" } resolution = 4.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Convert atoms to be neutral 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-4807/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: 5.38, per 1000 atoms: 0.42 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: 6.49 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: 1.28 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: 3.94 Time building geometry restraints manager: 6.73 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: 7510 28.64 - 57.28: 302 57.28 - 85.92: 114 85.92 - 114.56: 14 114.56 - 143.20: 3 Dihedral angle restraints: 7943 sinusoidal: 3359 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 7940 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 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. 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: 4.060 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: 0.000 Extract box with map and model: 19.760 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.000 Process input model: 38.050 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 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 : 3.644 27.314 17407 Z= 2.460 Chirality : 0.208 0.806 2000 Planarity : 0.031 0.256 2243 Dihedral : 18.704 143.201 4979 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 4.09 % Allowed : 6.42 % Favored : 89.50 % Rotamer Outliers : 3.66 % 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 *********************** 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 : 1.582 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 outliers start: 49 outliers final: 10 residues processed: 852 average time/residue: 0.3467 time to fit residues: 389.6458 Evaluate side-chains 620 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 610 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1910 time to fit residues: 5.4173 ------------------------------------------------------------------------------- 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: 0.9980 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 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** ** J 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 12881 Z= 0.332 Angle : 1.007 25.565 17407 Z= 0.511 Chirality : 0.050 0.260 2000 Planarity : 0.007 0.078 2243 Dihedral : 9.398 131.435 1757 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.79 % Favored : 92.39 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 2.22 % Twisted General : 0.46 % 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: -0.24 (0.18), residues: 784 sheet: -1.09 (0.40), residues: 135 loop : -2.00 (0.23), residues: 671 *********************** 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 757 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 746 time to evaluate : 2.218 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 outliers start: 11 outliers final: 3 residues processed: 750 average time/residue: 0.3644 time to fit residues: 360.2282 Evaluate side-chains 574 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 571 time to evaluate : 1.460 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1337 time to fit residues: 2.6858 ------------------------------------------------------------------------------- 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: 1.9990 chunk 43 optimal weight: 0.0970 chunk 117 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 12881 Z= 0.327 Angle : 0.935 25.789 17407 Z= 0.470 Chirality : 0.048 0.281 2000 Planarity : 0.007 0.087 2243 Dihedral : 8.668 132.096 1757 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 26.27 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.86 % Favored : 92.26 % Rotamer Outliers : 0.37 % 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: -1.40 (0.20), residues: 1590 helix: -0.30 (0.17), residues: 788 sheet: -1.05 (0.41), residues: 146 loop : -1.59 (0.25), residues: 656 *********************** 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 717 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 712 time to evaluate : 1.599 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 outliers start: 5 outliers final: 0 residues processed: 715 average time/residue: 0.3127 time to fit residues: 296.5636 Evaluate side-chains 563 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 563 time to evaluate : 1.599 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3031 ------------------------------------------------------------------------------- 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: 0.9980 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 0.0670 chunk 95 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 252 ASN ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN ** M 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.7264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 12881 Z= 0.294 Angle : 0.921 24.796 17407 Z= 0.459 Chirality : 0.050 0.463 2000 Planarity : 0.007 0.092 2243 Dihedral : 8.446 130.342 1757 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 26.03 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.23 % Favored : 92.89 % Rotamer Outliers : 0.37 % 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: -1.27 (0.21), residues: 1590 helix: -0.33 (0.18), residues: 786 sheet: -0.76 (0.42), residues: 150 loop : -1.39 (0.25), residues: 654 *********************** 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 690 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 685 time to evaluate : 1.486 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 outliers start: 5 outliers final: 0 residues processed: 686 average time/residue: 0.2942 time to fit residues: 272.6658 Evaluate side-chains 565 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 565 time to evaluate : 1.655 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2540 ------------------------------------------------------------------------------- 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: 0.8980 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 0.0980 chunk 112 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 GLN ** I 324 HIS ** 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 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.7761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 12881 Z= 0.308 Angle : 0.929 24.321 17407 Z= 0.460 Chirality : 0.051 0.535 2000 Planarity : 0.007 0.100 2243 Dihedral : 8.205 128.017 1757 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 28.37 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.11 % Favored : 92.08 % Rotamer Outliers : 0.22 % 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: -1.39 (0.21), residues: 1590 helix: -0.54 (0.17), residues: 783 sheet: -0.60 (0.43), residues: 152 loop : -1.33 (0.26), residues: 655 *********************** 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 681 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 678 time to evaluate : 1.616 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 outliers start: 3 outliers final: 1 residues processed: 680 average time/residue: 0.3024 time to fit residues: 277.1783 Evaluate side-chains 560 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 559 time to evaluate : 1.610 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1570 time to fit residues: 2.4926 ------------------------------------------------------------------------------- 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: 0.0970 chunk 135 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 0.0070 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 319 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** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.8060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 12881 Z= 0.272 Angle : 0.928 23.555 17407 Z= 0.458 Chirality : 0.051 0.510 2000 Planarity : 0.007 0.111 2243 Dihedral : 7.992 127.024 1757 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.42 % Favored : 91.76 % Rotamer Outliers : 0.22 % 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: -1.30 (0.21), residues: 1590 helix: -0.46 (0.18), residues: 779 sheet: -0.58 (0.43), residues: 151 loop : -1.30 (0.26), residues: 660 *********************** 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 673 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 670 time to evaluate : 1.613 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 outliers start: 3 outliers final: 2 residues processed: 672 average time/residue: 0.3056 time to fit residues: 279.7749 Evaluate side-chains 560 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 558 time to evaluate : 1.621 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1597 time to fit residues: 2.8161 ------------------------------------------------------------------------------- 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: 0.2980 chunk 17 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 69 optimal weight: 0.0770 chunk 93 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 319 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 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 267 GLN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.8439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 12881 Z= 0.285 Angle : 0.926 22.949 17407 Z= 0.460 Chirality : 0.051 0.526 2000 Planarity : 0.006 0.090 2243 Dihedral : 7.930 126.338 1757 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 27.67 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.74 % Favored : 91.51 % Rotamer Outliers : 0.07 % 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: -1.37 (0.21), residues: 1590 helix: -0.61 (0.18), residues: 789 sheet: -0.42 (0.43), residues: 155 loop : -1.27 (0.27), residues: 646 *********************** 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 658 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 657 time to evaluate : 1.562 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 outliers start: 1 outliers final: 1 residues processed: 657 average time/residue: 0.2954 time to fit residues: 262.7245 Evaluate side-chains 546 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 545 time to evaluate : 1.583 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1515 time to fit residues: 2.4424 ------------------------------------------------------------------------------- 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: 2.9990 chunk 89 optimal weight: 0.0770 chunk 45 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 102 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 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 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: 0.6207 moved from start: 0.8714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 12881 Z= 0.288 Angle : 0.945 21.799 17407 Z= 0.473 Chirality : 0.051 0.513 2000 Planarity : 0.007 0.100 2243 Dihedral : 7.989 126.158 1757 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 28.76 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.86 % Favored : 91.45 % Rotamer Outliers : 0.07 % 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: -1.45 (0.21), residues: 1590 helix: -0.66 (0.18), residues: 788 sheet: -0.78 (0.44), residues: 139 loop : -1.22 (0.26), residues: 663 *********************** 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 657 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 656 time to evaluate : 1.589 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 outliers start: 1 outliers final: 1 residues processed: 656 average time/residue: 0.3020 time to fit residues: 271.6656 Evaluate side-chains 543 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 542 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1605 time to fit residues: 2.4604 ------------------------------------------------------------------------------- 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: 0.0370 chunk 140 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 126 optimal weight: 0.2980 chunk 132 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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** ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN K 319 GLN ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN J 197 ASN ** 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: 0.6203 moved from start: 0.8941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 12881 Z= 0.300 Angle : 0.978 27.512 17407 Z= 0.486 Chirality : 0.052 0.517 2000 Planarity : 0.006 0.083 2243 Dihedral : 7.902 125.759 1757 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 29.77 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.74 % Favored : 91.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.67 (0.18), residues: 769 sheet: -0.42 (0.43), residues: 150 loop : -1.25 (0.26), residues: 671 *********************** 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 658 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 658 time to evaluate : 1.553 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 outliers start: 0 outliers final: 0 residues processed: 658 average time/residue: 0.2897 time to fit residues: 260.5135 Evaluate side-chains 560 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 560 time to evaluate : 1.602 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1594 ------------------------------------------------------------------------------- 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: 0.1980 chunk 90 optimal weight: 0.7980 chunk 70 optimal weight: 0.0000 chunk 102 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 98 optimal weight: 0.1980 overall best weight: 0.3184 ------------------------------------------------------------------------------- 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** ** H 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN J 197 ASN ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.9123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 12881 Z= 0.288 Angle : 1.003 27.197 17407 Z= 0.500 Chirality : 0.053 0.515 2000 Planarity : 0.007 0.120 2243 Dihedral : 7.943 125.392 1757 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 28.95 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.05 % Favored : 91.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.52 (0.21), residues: 1590 helix: -0.75 (0.18), residues: 759 sheet: -0.38 (0.43), residues: 149 loop : -1.33 (0.26), residues: 682 ********************** 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 653 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 653 time to evaluate : 1.526 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 outliers start: 0 outliers final: 0 residues processed: 653 average time/residue: 0.2866 time to fit residues: 255.9076 Evaluate side-chains 542 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 542 time to evaluate : 1.562 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1660 ------------------------------------------------------------------------------- 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: 0.9990 chunk 37 optimal weight: 0.4980 chunk 114 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN J 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.132388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107393 restraints weight = 34548.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110783 restraints weight = 25779.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113489 restraints weight = 20121.285| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.9334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 12881 Z= 0.305 Angle : 1.006 27.163 17407 Z= 0.502 Chirality : 0.053 0.487 2000 Planarity : 0.007 0.112 2243 Dihedral : 7.947 125.297 1757 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 31.29 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.74 % Favored : 91.57 % Rotamer Outliers : 0.00 % 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: -1.56 (0.21), residues: 1590 helix: -0.77 (0.18), residues: 761 sheet: -0.35 (0.42), residues: 149 loop : -1.36 (0.26), residues: 680 =============================================================================== Job complete usr+sys time: 4720.93 seconds wall clock time: 85 minutes 20.39 seconds (5120.39 seconds total)