Starting phenix.real_space_refine on Thu Feb 15 19:31:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsr_32114/02_2024/7vsr_32114_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsr_32114/02_2024/7vsr_32114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsr_32114/02_2024/7vsr_32114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsr_32114/02_2024/7vsr_32114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsr_32114/02_2024/7vsr_32114_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsr_32114/02_2024/7vsr_32114_trim_updated.pdb" } resolution = 4.5 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= 0.004 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: 7 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 154 5.16 5 C 21400 2.51 5 N 5606 2.21 5 O 6222 1.98 5 H 32736 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 444": "OD1" <-> "OD2" Residue "M TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 66142 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4722 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "B" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4722 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "C" Number of atoms: 4721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4721 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "D" Number of atoms: 4632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4632 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "E" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4639 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "F" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4644 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "G" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4722 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "H" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4722 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "I" Number of atoms: 4721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4721 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "J" Number of atoms: 4632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4632 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "K" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4639 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "L" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4644 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "M" Number of atoms: 4892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 4892 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain breaks: 3 Chain: "N" Number of atoms: 4892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 4892 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain breaks: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.73, per 1000 atoms: 0.31 Number of scatterers: 66142 At special positions: 0 Unit cell: (160.5, 167.99, 125.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 154 16.00 P 18 15.00 Mg 6 11.99 O 6222 8.00 N 5606 7.00 C 21400 6.00 H 32736 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 37.93 Conformation dependent library (CDL) restraints added in 4.8 seconds 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 206 helices and 28 sheets defined 45.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.85 Creating SS restraints... Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.540A pdb=" N ASN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 207 through 219 removed outlier: 3.636A pdb=" N ARG A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 258 through 268 removed outlier: 3.775A pdb=" N GLU A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 286 through 289 No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 291 through 294 Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.735A pdb=" N ARG A 348 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 349' Processing helix chain 'A' and resid 362 through 370 Processing helix chain 'A' and resid 375 through 394 Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 408 through 411 No H-bonds generated for 'chain 'A' and resid 408 through 411' Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'B' and resid 170 through 175 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 207 through 219 removed outlier: 3.673A pdb=" N ARG B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'B' and resid 258 through 268 Processing helix chain 'B' and resid 286 through 296 removed outlier: 6.400A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N MET B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N MET B 295 " --> pdb=" O GLY B 291 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 344 through 347 No H-bonds generated for 'chain 'B' and resid 344 through 347' Processing helix chain 'B' and resid 362 through 371 removed outlier: 3.720A pdb=" N LYS B 371 " --> pdb=" O PHE B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 394 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 408 through 411 No H-bonds generated for 'chain 'B' and resid 408 through 411' Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 433 through 441 Processing helix chain 'B' and resid 445 through 456 Processing helix chain 'C' and resid 170 through 174 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 207 through 219 removed outlier: 4.006A pdb=" N ARG C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 No H-bonds generated for 'chain 'C' and resid 238 through 241' Processing helix chain 'C' and resid 258 through 268 Processing helix chain 'C' and resid 286 through 296 removed outlier: 6.406A pdb=" N GLU C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N MET C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N MET C 295 " --> pdb=" O GLY C 291 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 344 through 349 removed outlier: 3.676A pdb=" N ARG C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 370 Processing helix chain 'C' and resid 375 through 394 Processing helix chain 'C' and resid 401 through 403 No H-bonds generated for 'chain 'C' and resid 401 through 403' Processing helix chain 'C' and resid 408 through 411 No H-bonds generated for 'chain 'C' and resid 408 through 411' Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 433 through 440 Processing helix chain 'C' and resid 445 through 456 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 207 through 219 Processing helix chain 'D' and resid 238 through 241 No H-bonds generated for 'chain 'D' and resid 238 through 241' Processing helix chain 'D' and resid 258 through 268 Processing helix chain 'D' and resid 286 through 296 removed outlier: 6.360A pdb=" N GLU D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N MET D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N MET D 295 " --> pdb=" O GLY D 291 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 362 through 371 Processing helix chain 'D' and resid 375 through 394 Processing helix chain 'D' and resid 401 through 403 No H-bonds generated for 'chain 'D' and resid 401 through 403' Processing helix chain 'D' and resid 408 through 411 No H-bonds generated for 'chain 'D' and resid 408 through 411' Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'D' and resid 433 through 440 Processing helix chain 'D' and resid 445 through 456 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.798A pdb=" N ILE E 193 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 219 Processing helix chain 'E' and resid 238 through 241 No H-bonds generated for 'chain 'E' and resid 238 through 241' Processing helix chain 'E' and resid 258 through 268 removed outlier: 3.980A pdb=" N GLU E 268 " --> pdb=" O GLN E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 removed outlier: 7.155A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL E 293 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N MET E 294 " --> pdb=" O PHE E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 344 through 349 Processing helix chain 'E' and resid 362 through 369 Processing helix chain 'E' and resid 375 through 394 Processing helix chain 'E' and resid 401 through 403 No H-bonds generated for 'chain 'E' and resid 401 through 403' Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 422 through 431 Processing helix chain 'E' and resid 433 through 441 Processing helix chain 'E' and resid 445 through 456 Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 207 through 219 Processing helix chain 'F' and resid 238 through 241 No H-bonds generated for 'chain 'F' and resid 238 through 241' Processing helix chain 'F' and resid 259 through 268 removed outlier: 3.676A pdb=" N GLU F 268 " --> pdb=" O GLN F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 294 removed outlier: 7.059A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL F 293 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET F 294 " --> pdb=" O PHE F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 306 No H-bonds generated for 'chain 'F' and resid 304 through 306' Processing helix chain 'F' and resid 344 through 349 removed outlier: 3.915A pdb=" N ARG F 349 " --> pdb=" O ALA F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 370 Processing helix chain 'F' and resid 375 through 394 Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 408 through 411 No H-bonds generated for 'chain 'F' and resid 408 through 411' Processing helix chain 'F' and resid 422 through 431 removed outlier: 4.020A pdb=" N GLU F 427 " --> pdb=" O GLN F 423 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE F 428 " --> pdb=" O TRP F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 440 Processing helix chain 'F' and resid 445 through 456 removed outlier: 3.658A pdb=" N LEU F 455 " --> pdb=" O TRP F 451 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU F 456 " --> pdb=" O THR F 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 176 removed outlier: 3.550A pdb=" N ASN G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP G 176 " --> pdb=" O ASP G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 207 through 219 removed outlier: 3.667A pdb=" N ARG G 212 " --> pdb=" O THR G 208 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG G 213 " --> pdb=" O PHE G 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR G 216 " --> pdb=" O ARG G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 241 No H-bonds generated for 'chain 'G' and resid 238 through 241' Processing helix chain 'G' and resid 258 through 268 removed outlier: 3.776A pdb=" N GLU G 268 " --> pdb=" O GLN G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 283 No H-bonds generated for 'chain 'G' and resid 281 through 283' Processing helix chain 'G' and resid 286 through 289 No H-bonds generated for 'chain 'G' and resid 286 through 289' Processing helix chain 'G' and resid 291 through 294 Processing helix chain 'G' and resid 304 through 306 No H-bonds generated for 'chain 'G' and resid 304 through 306' Processing helix chain 'G' and resid 338 through 340 No H-bonds generated for 'chain 'G' and resid 338 through 340' Processing helix chain 'G' and resid 344 through 349 removed outlier: 3.695A pdb=" N ARG G 348 " --> pdb=" O TYR G 344 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG G 349 " --> pdb=" O ALA G 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 344 through 349' Processing helix chain 'G' and resid 362 through 370 Processing helix chain 'G' and resid 375 through 394 Processing helix chain 'G' and resid 401 through 403 No H-bonds generated for 'chain 'G' and resid 401 through 403' Processing helix chain 'G' and resid 422 through 431 Processing helix chain 'G' and resid 433 through 440 Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'H' and resid 170 through 174 Processing helix chain 'H' and resid 181 through 194 Processing helix chain 'H' and resid 207 through 219 removed outlier: 3.819A pdb=" N ARG H 212 " --> pdb=" O THR H 208 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG H 213 " --> pdb=" O PHE H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 226 No H-bonds generated for 'chain 'H' and resid 224 through 226' Processing helix chain 'H' and resid 238 through 241 No H-bonds generated for 'chain 'H' and resid 238 through 241' Processing helix chain 'H' and resid 258 through 268 removed outlier: 3.743A pdb=" N GLU H 268 " --> pdb=" O GLN H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 296 removed outlier: 6.835A pdb=" N GLU H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL H 293 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET H 294 " --> pdb=" O PHE H 290 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET H 295 " --> pdb=" O GLY H 291 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU H 296 " --> pdb=" O GLU H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 306 No H-bonds generated for 'chain 'H' and resid 304 through 306' Processing helix chain 'H' and resid 344 through 349 removed outlier: 3.509A pdb=" N ARG H 349 " --> pdb=" O ALA H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 371 removed outlier: 3.569A pdb=" N LYS H 371 " --> pdb=" O PHE H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 394 Processing helix chain 'H' and resid 401 through 403 No H-bonds generated for 'chain 'H' and resid 401 through 403' Processing helix chain 'H' and resid 408 through 411 No H-bonds generated for 'chain 'H' and resid 408 through 411' Processing helix chain 'H' and resid 422 through 431 Processing helix chain 'H' and resid 433 through 441 Processing helix chain 'H' and resid 445 through 456 Processing helix chain 'I' and resid 171 through 174 No H-bonds generated for 'chain 'I' and resid 171 through 174' Processing helix chain 'I' and resid 181 through 194 Processing helix chain 'I' and resid 207 through 219 removed outlier: 3.967A pdb=" N ARG I 212 " --> pdb=" O THR I 208 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG I 213 " --> pdb=" O PHE I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 226 No H-bonds generated for 'chain 'I' and resid 224 through 226' Processing helix chain 'I' and resid 238 through 241 No H-bonds generated for 'chain 'I' and resid 238 through 241' Processing helix chain 'I' and resid 258 through 268 Processing helix chain 'I' and resid 281 through 283 No H-bonds generated for 'chain 'I' and resid 281 through 283' Processing helix chain 'I' and resid 286 through 296 removed outlier: 6.677A pdb=" N GLU I 292 " --> pdb=" O LYS I 288 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET I 294 " --> pdb=" O PHE I 290 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET I 295 " --> pdb=" O GLY I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 306 No H-bonds generated for 'chain 'I' and resid 304 through 306' Processing helix chain 'I' and resid 344 through 348 Processing helix chain 'I' and resid 362 through 370 Processing helix chain 'I' and resid 375 through 394 Processing helix chain 'I' and resid 401 through 403 No H-bonds generated for 'chain 'I' and resid 401 through 403' Processing helix chain 'I' and resid 408 through 411 No H-bonds generated for 'chain 'I' and resid 408 through 411' Processing helix chain 'I' and resid 422 through 431 Processing helix chain 'I' and resid 433 through 440 Processing helix chain 'I' and resid 445 through 456 Processing helix chain 'J' and resid 181 through 194 Processing helix chain 'J' and resid 207 through 219 Processing helix chain 'J' and resid 238 through 241 No H-bonds generated for 'chain 'J' and resid 238 through 241' Processing helix chain 'J' and resid 258 through 268 Processing helix chain 'J' and resid 281 through 283 No H-bonds generated for 'chain 'J' and resid 281 through 283' Processing helix chain 'J' and resid 286 through 296 removed outlier: 7.242A pdb=" N GLU J 292 " --> pdb=" O LYS J 288 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL J 293 " --> pdb=" O VAL J 289 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET J 294 " --> pdb=" O PHE J 290 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N MET J 295 " --> pdb=" O GLY J 291 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU J 296 " --> pdb=" O GLU J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 306 No H-bonds generated for 'chain 'J' and resid 304 through 306' Processing helix chain 'J' and resid 344 through 349 removed outlier: 3.663A pdb=" N ARG J 349 " --> pdb=" O ALA J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 370 Processing helix chain 'J' and resid 375 through 394 Processing helix chain 'J' and resid 401 through 403 No H-bonds generated for 'chain 'J' and resid 401 through 403' Processing helix chain 'J' and resid 408 through 411 No H-bonds generated for 'chain 'J' and resid 408 through 411' Processing helix chain 'J' and resid 422 through 431 Processing helix chain 'J' and resid 433 through 440 Processing helix chain 'J' and resid 445 through 456 Processing helix chain 'K' and resid 181 through 194 Processing helix chain 'K' and resid 207 through 219 Processing helix chain 'K' and resid 238 through 241 No H-bonds generated for 'chain 'K' and resid 238 through 241' Processing helix chain 'K' and resid 258 through 268 removed outlier: 3.805A pdb=" N GLU K 268 " --> pdb=" O GLN K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 283 No H-bonds generated for 'chain 'K' and resid 281 through 283' Processing helix chain 'K' and resid 286 through 296 removed outlier: 7.903A pdb=" N GLU K 292 " --> pdb=" O LYS K 288 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL K 293 " --> pdb=" O VAL K 289 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N MET K 294 " --> pdb=" O PHE K 290 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N MET K 295 " --> pdb=" O GLY K 291 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU K 296 " --> pdb=" O GLU K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 306 No H-bonds generated for 'chain 'K' and resid 304 through 306' Processing helix chain 'K' and resid 344 through 349 Processing helix chain 'K' and resid 362 through 371 removed outlier: 3.607A pdb=" N LYS K 371 " --> pdb=" O PHE K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 375 through 394 Processing helix chain 'K' and resid 401 through 403 No H-bonds generated for 'chain 'K' and resid 401 through 403' Processing helix chain 'K' and resid 408 through 411 No H-bonds generated for 'chain 'K' and resid 408 through 411' Processing helix chain 'K' and resid 422 through 441 removed outlier: 4.461A pdb=" N ALA K 434 " --> pdb=" O MET K 430 " (cutoff:3.500A) Proline residue: K 435 - end of helix Processing helix chain 'K' and resid 445 through 456 Processing helix chain 'L' and resid 181 through 193 Processing helix chain 'L' and resid 207 through 219 Processing helix chain 'L' and resid 238 through 241 No H-bonds generated for 'chain 'L' and resid 238 through 241' Processing helix chain 'L' and resid 259 through 268 removed outlier: 3.652A pdb=" N GLU L 268 " --> pdb=" O GLN L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 281 through 283 No H-bonds generated for 'chain 'L' and resid 281 through 283' Processing helix chain 'L' and resid 286 through 296 removed outlier: 7.541A pdb=" N GLU L 292 " --> pdb=" O LYS L 288 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL L 293 " --> pdb=" O VAL L 289 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N MET L 294 " --> pdb=" O PHE L 290 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N MET L 295 " --> pdb=" O GLY L 291 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU L 296 " --> pdb=" O GLU L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 301 No H-bonds generated for 'chain 'L' and resid 299 through 301' Processing helix chain 'L' and resid 304 through 306 No H-bonds generated for 'chain 'L' and resid 304 through 306' Processing helix chain 'L' and resid 344 through 349 removed outlier: 3.540A pdb=" N ARG L 349 " --> pdb=" O ALA L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 370 Processing helix chain 'L' and resid 375 through 394 Processing helix chain 'L' and resid 401 through 403 No H-bonds generated for 'chain 'L' and resid 401 through 403' Processing helix chain 'L' and resid 408 through 411 No H-bonds generated for 'chain 'L' and resid 408 through 411' Processing helix chain 'L' and resid 422 through 431 Processing helix chain 'L' and resid 433 through 440 Processing helix chain 'L' and resid 445 through 456 Processing helix chain 'M' and resid 8 through 19 removed outlier: 3.919A pdb=" N TYR M 13 " --> pdb=" O ARG M 9 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET M 14 " --> pdb=" O ASN M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 56 removed outlier: 3.687A pdb=" N LEU M 51 " --> pdb=" O ASN M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 80 Processing helix chain 'M' and resid 86 through 98 Processing helix chain 'M' and resid 109 through 117 removed outlier: 3.687A pdb=" N ASN M 116 " --> pdb=" O PHE M 112 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY M 117 " --> pdb=" O SER M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 136 Processing helix chain 'M' and resid 156 through 174 removed outlier: 3.564A pdb=" N ARG M 172 " --> pdb=" O TYR M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 227 No H-bonds generated for 'chain 'M' and resid 224 through 227' Processing helix chain 'M' and resid 239 through 250 removed outlier: 3.984A pdb=" N MET M 245 " --> pdb=" O TYR M 242 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER M 250 " --> pdb=" O TYR M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 309 Processing helix chain 'N' and resid 8 through 19 removed outlier: 3.871A pdb=" N TYR N 13 " --> pdb=" O ARG N 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET N 14 " --> pdb=" O ASN N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.671A pdb=" N LEU N 51 " --> pdb=" O ASN N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 80 Processing helix chain 'N' and resid 86 through 98 Processing helix chain 'N' and resid 109 through 117 removed outlier: 3.671A pdb=" N ASN N 116 " --> pdb=" O PHE N 112 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLY N 117 " --> pdb=" O SER N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 136 Processing helix chain 'N' and resid 152 through 154 No H-bonds generated for 'chain 'N' and resid 152 through 154' Processing helix chain 'N' and resid 156 through 174 removed outlier: 3.552A pdb=" N ARG N 172 " --> pdb=" O TYR N 168 " (cutoff:3.500A) Processing helix chain 'N' and resid 224 through 227 No H-bonds generated for 'chain 'N' and resid 224 through 227' Processing helix chain 'N' and resid 239 through 250 removed outlier: 3.995A pdb=" N MET N 245 " --> pdb=" O TYR N 242 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER N 250 " --> pdb=" O TYR N 247 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 309 Processing sheet with id= A, first strand: chain 'A' and resid 351 through 354 removed outlier: 9.282A pdb=" N ILE A 197 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A 328 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU A 199 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY A 330 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N GLY A 201 " --> pdb=" O GLY A 330 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N MET A 332 " --> pdb=" O GLY A 201 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR A 274 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE A 329 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N PHE A 276 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU A 331 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 278 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ASN A 333 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 243 through 247 Processing sheet with id= C, first strand: chain 'B' and resid 351 through 355 removed outlier: 8.978A pdb=" N ILE B 197 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE B 328 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU B 199 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY B 330 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLY B 201 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N MET B 332 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR B 274 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE B 329 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE B 276 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU B 331 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE B 278 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ASN B 333 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 243 through 247 Processing sheet with id= E, first strand: chain 'C' and resid 351 through 354 removed outlier: 9.036A pdb=" N ILE C 197 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 328 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU C 199 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY C 330 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLY C 201 " --> pdb=" O GLY C 330 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N MET C 332 " --> pdb=" O GLY C 201 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR C 274 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE C 329 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE C 276 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU C 331 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 278 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ASN C 333 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 243 through 247 Processing sheet with id= G, first strand: chain 'D' and resid 351 through 355 removed outlier: 3.674A pdb=" N SER D 351 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE D 328 " --> pdb=" O ILE D 197 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU D 199 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY D 330 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLY D 201 " --> pdb=" O GLY D 330 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N MET D 332 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 245 through 247 Processing sheet with id= I, first strand: chain 'E' and resid 351 through 354 removed outlier: 3.671A pdb=" N SER E 351 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ILE E 197 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE E 328 " --> pdb=" O ILE E 197 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU E 199 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY E 330 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR E 274 " --> pdb=" O TYR E 327 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE E 329 " --> pdb=" O TYR E 274 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N PHE E 276 " --> pdb=" O ILE E 329 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU E 331 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE E 278 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 243 through 247 Processing sheet with id= K, first strand: chain 'F' and resid 351 through 353 removed outlier: 9.012A pdb=" N ILE F 197 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE F 328 " --> pdb=" O ILE F 197 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU F 199 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY F 330 " --> pdb=" O LEU F 199 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR F 274 " --> pdb=" O TYR F 327 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE F 329 " --> pdb=" O TYR F 274 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PHE F 276 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU F 331 " --> pdb=" O PHE F 276 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE F 278 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 243 through 247 Processing sheet with id= M, first strand: chain 'G' and resid 351 through 354 removed outlier: 9.268A pdb=" N ILE G 197 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE G 328 " --> pdb=" O ILE G 197 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU G 199 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLY G 330 " --> pdb=" O LEU G 199 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR G 274 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE G 329 " --> pdb=" O TYR G 274 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE G 276 " --> pdb=" O ILE G 329 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU G 331 " --> pdb=" O PHE G 276 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE G 278 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 243 through 247 Processing sheet with id= O, first strand: chain 'H' and resid 351 through 355 removed outlier: 8.897A pdb=" N ILE H 197 " --> pdb=" O VAL H 326 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE H 328 " --> pdb=" O ILE H 197 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU H 199 " --> pdb=" O ILE H 328 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLY H 330 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLY H 201 " --> pdb=" O GLY H 330 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N MET H 332 " --> pdb=" O GLY H 201 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR H 274 " --> pdb=" O TYR H 327 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE H 329 " --> pdb=" O TYR H 274 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N PHE H 276 " --> pdb=" O ILE H 329 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU H 331 " --> pdb=" O PHE H 276 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE H 278 " --> pdb=" O LEU H 331 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ASN H 333 " --> pdb=" O ILE H 278 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 243 through 247 Processing sheet with id= Q, first strand: chain 'I' and resid 351 through 354 removed outlier: 9.274A pdb=" N ILE I 197 " --> pdb=" O VAL I 326 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE I 328 " --> pdb=" O ILE I 197 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU I 199 " --> pdb=" O ILE I 328 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY I 330 " --> pdb=" O LEU I 199 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLY I 201 " --> pdb=" O GLY I 330 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N MET I 332 " --> pdb=" O GLY I 201 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR I 274 " --> pdb=" O TYR I 327 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE I 329 " --> pdb=" O TYR I 274 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE I 276 " --> pdb=" O ILE I 329 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU I 331 " --> pdb=" O PHE I 276 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE I 278 " --> pdb=" O LEU I 331 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASN I 333 " --> pdb=" O ILE I 278 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 243 through 247 Processing sheet with id= S, first strand: chain 'J' and resid 351 through 354 removed outlier: 9.045A pdb=" N ILE J 197 " --> pdb=" O VAL J 326 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE J 328 " --> pdb=" O ILE J 197 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU J 199 " --> pdb=" O ILE J 328 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY J 330 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR J 274 " --> pdb=" O TYR J 327 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE J 329 " --> pdb=" O TYR J 274 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE J 276 " --> pdb=" O ILE J 329 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU J 331 " --> pdb=" O PHE J 276 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE J 278 " --> pdb=" O LEU J 331 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 243 through 247 removed outlier: 3.594A pdb=" N GLY J 244 " --> pdb=" O LYS J 255 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 351 through 354 removed outlier: 8.722A pdb=" N ILE K 197 " --> pdb=" O VAL K 326 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE K 328 " --> pdb=" O ILE K 197 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU K 199 " --> pdb=" O ILE K 328 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY K 330 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR K 274 " --> pdb=" O TYR K 327 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE K 329 " --> pdb=" O TYR K 274 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N PHE K 276 " --> pdb=" O ILE K 329 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU K 331 " --> pdb=" O PHE K 276 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE K 278 " --> pdb=" O LEU K 331 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 243 through 247 Processing sheet with id= W, first strand: chain 'L' and resid 351 through 353 removed outlier: 9.032A pdb=" N ILE L 197 " --> pdb=" O VAL L 326 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE L 328 " --> pdb=" O ILE L 197 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU L 199 " --> pdb=" O ILE L 328 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLY L 330 " --> pdb=" O LEU L 199 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR L 274 " --> pdb=" O TYR L 327 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE L 329 " --> pdb=" O TYR L 274 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE L 276 " --> pdb=" O ILE L 329 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU L 331 " --> pdb=" O PHE L 276 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE L 278 " --> pdb=" O LEU L 331 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 243 through 247 Processing sheet with id= Y, first strand: chain 'M' and resid 179 through 181 Processing sheet with id= Z, first strand: chain 'M' and resid 215 through 221 removed outlier: 3.692A pdb=" N LYS M 221 " --> pdb=" O ILE M 264 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASP M 282 " --> pdb=" O GLY M 261 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU M 263 " --> pdb=" O ASP M 282 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLY M 284 " --> pdb=" O LEU M 263 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N TYR M 265 " --> pdb=" O GLY M 284 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS M 286 " --> pdb=" O TYR M 265 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N HIS M 267 " --> pdb=" O CYS M 286 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL M 288 " --> pdb=" O HIS M 267 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'N' and resid 179 through 181 Processing sheet with id= AB, first strand: chain 'N' and resid 215 through 221 removed outlier: 3.679A pdb=" N LYS N 221 " --> pdb=" O ILE N 264 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASP N 282 " --> pdb=" O GLY N 261 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU N 263 " --> pdb=" O ASP N 282 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLY N 284 " --> pdb=" O LEU N 263 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR N 265 " --> pdb=" O GLY N 284 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N CYS N 286 " --> pdb=" O TYR N 265 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N HIS N 267 " --> pdb=" O CYS N 286 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL N 288 " --> pdb=" O HIS N 267 " (cutoff:3.500A) 1132 hydrogen bonds defined for protein. 3306 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: 20.18 Time building geometry restraints manager: 40.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 32674 1.03 - 1.23: 289 1.23 - 1.43: 14404 1.43 - 1.62: 19297 1.62 - 1.82: 258 Bond restraints: 66922 Sorted by residual: bond pdb=" N3B GNP I1001 " pdb=" PG GNP I1001 " ideal model delta sigma weight residual 1.801 1.625 0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" N3B GNP H1001 " pdb=" PG GNP H1001 " ideal model delta sigma weight residual 1.801 1.626 0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" N3B GNP C1001 " pdb=" PG GNP C1001 " ideal model delta sigma weight residual 1.801 1.627 0.174 2.00e-02 2.50e+03 7.60e+01 bond pdb=" N3B GNP B1001 " pdb=" PG GNP B1001 " ideal model delta sigma weight residual 1.801 1.627 0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" N3B GNP A1001 " pdb=" PG GNP A1001 " ideal model delta sigma weight residual 1.801 1.628 0.173 2.00e-02 2.50e+03 7.48e+01 ... (remaining 66917 not shown) Histogram of bond angle deviations from ideal: 98.47 - 105.61: 807 105.61 - 112.75: 76167 112.75 - 119.89: 18875 119.89 - 127.03: 24516 127.03 - 134.17: 383 Bond angle restraints: 120748 Sorted by residual: angle pdb=" N VAL A 289 " pdb=" CA VAL A 289 " pdb=" C VAL A 289 " ideal model delta sigma weight residual 111.45 107.68 3.77 9.30e-01 1.16e+00 1.65e+01 angle pdb=" N LEU I 346 " pdb=" CA LEU I 346 " pdb=" C LEU I 346 " ideal model delta sigma weight residual 111.36 106.97 4.39 1.09e+00 8.42e-01 1.62e+01 angle pdb=" CA GLY J 244 " pdb=" C GLY J 244 " pdb=" N TYR J 245 " ideal model delta sigma weight residual 114.67 119.14 -4.47 1.11e+00 8.12e-01 1.62e+01 angle pdb=" N GLY I 249 " pdb=" CA GLY I 249 " pdb=" C GLY I 249 " ideal model delta sigma weight residual 113.18 103.70 9.48 2.37e+00 1.78e-01 1.60e+01 angle pdb=" N ALA I 345 " pdb=" CA ALA I 345 " pdb=" C ALA I 345 " ideal model delta sigma weight residual 111.28 107.20 4.08 1.09e+00 8.42e-01 1.40e+01 ... (remaining 120743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 28567 17.60 - 35.19: 2315 35.19 - 52.79: 574 52.79 - 70.38: 123 70.38 - 87.98: 15 Dihedral angle restraints: 31594 sinusoidal: 17236 harmonic: 14358 Sorted by residual: dihedral pdb=" CA ASN B 285 " pdb=" C ASN B 285 " pdb=" N LEU B 286 " pdb=" CA LEU B 286 " ideal model delta harmonic sigma weight residual -180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ASN L 370 " pdb=" C ASN L 370 " pdb=" N LYS L 371 " pdb=" CA LYS L 371 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ALA K 335 " pdb=" C ALA K 335 " pdb=" N ASP K 336 " pdb=" CA ASP K 336 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 31591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3486 0.036 - 0.071: 912 0.071 - 0.107: 367 0.107 - 0.142: 106 0.142 - 0.178: 15 Chirality restraints: 4886 Sorted by residual: chirality pdb=" CA ARG I 283 " pdb=" N ARG I 283 " pdb=" C ARG I 283 " pdb=" CB ARG I 283 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CA ARG K 349 " pdb=" N ARG K 349 " pdb=" C ARG K 349 " pdb=" CB ARG K 349 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA TRP H 306 " pdb=" N TRP H 306 " pdb=" C TRP H 306 " pdb=" CB TRP H 306 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 4883 not shown) Planarity restraints: 9808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 287 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C SER B 287 " 0.056 2.00e-02 2.50e+03 pdb=" O SER B 287 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS B 288 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 287 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.91e+00 pdb=" C SER C 287 " 0.052 2.00e-02 2.50e+03 pdb=" O SER C 287 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS C 288 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 450 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C LYS I 450 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS I 450 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP I 451 " 0.017 2.00e-02 2.50e+03 ... (remaining 9805 not shown) Histogram of nonbonded interaction distances: 1.30 - 1.96: 729 1.96 - 2.62: 84337 2.62 - 3.28: 203451 3.28 - 3.94: 244454 3.94 - 4.60: 397244 Nonbonded interactions: 930215 Sorted by model distance: nonbonded pdb=" O PHE B 441 " pdb="HH12 ARG M 122 " model vdw 1.305 1.850 nonbonded pdb=" O ILE H 242 " pdb=" H GLY H 257 " model vdw 1.410 1.850 nonbonded pdb=" O ILE E 242 " pdb=" H GLY E 257 " model vdw 1.413 1.850 nonbonded pdb=" H ASN H 248 " pdb=" O GLY H 251 " model vdw 1.419 1.850 nonbonded pdb=" O PHE H 441 " pdb="HH12 ARG N 122 " model vdw 1.425 1.850 ... (remaining 930210 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 233 or (resid 234 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name NE2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 235 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) \ or resid 256 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through \ 346 or (resid 347 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE or name HH11 or name HH12)) or resid 348 through 406 or (resid 407 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1)) or resid 408 through 457)) selection = (chain 'B' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 233 or (resid 234 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name NE2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 235 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) \ or resid 256 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through \ 346 or (resid 347 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE or name HH11 or name HH12)) or resid 348 through 406 or (resid 407 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1)) or resid 408 through 457)) selection = (chain 'C' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 233 or (resid 234 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name NE2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 235 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) \ or resid 256 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through \ 346 or (resid 347 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE or name HH11 or name HH12)) or resid 348 through 457)) selection = (chain 'D' and (resid 174 through 207 or (resid 208 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 209 through 254 or (resid 25 \ 5 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name CE or name NZ or name H or name HA or name HB2 or name HB3 or name HG2 or \ name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) or resid \ 256 through 340 or (resid 341 and (name N or name CA or name C or name O or name \ CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or n \ ame HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through 346 or (r \ esid 347 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name \ HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or na \ me HH11 or name HH12)) or resid 348 through 457)) selection = (chain 'E' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 233 or (resid 234 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name OE1 o \ r name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3) \ ) or resid 235 through 457)) selection = (chain 'F' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 233 or (resid 234 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name OE1 o \ r name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3) \ ) or resid 235 through 254 or (resid 255 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ3)) or resid 256 through 340 or (resid 341 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2 or name HA or \ name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG22 or nam \ e HG23)) or resid 342 through 346 or (resid 347 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 348 throu \ gh 457)) selection = (chain 'G' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 233 or (resid 234 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name NE2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 235 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) \ or resid 256 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through \ 346 or (resid 347 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE or name HH11 or name HH12)) or resid 348 through 406 or (resid 407 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1)) or resid 408 through 457)) selection = (chain 'H' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 233 or (resid 234 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name NE2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 235 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) \ or resid 256 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through \ 346 or (resid 347 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE or name HH11 or name HH12)) or resid 348 through 406 or (resid 407 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1)) or resid 408 through 457)) selection = (chain 'I' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 233 or (resid 234 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name NE2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 235 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) \ or resid 256 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through \ 346 or (resid 347 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE or name HH11 or name HH12)) or resid 348 through 457)) selection = (chain 'J' and (resid 174 through 207 or (resid 208 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 209 through 254 or (resid 25 \ 5 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name CE or name NZ or name H or name HA or name HB2 or name HB3 or name HG2 or \ name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) or resid \ 256 through 340 or (resid 341 and (name N or name CA or name C or name O or name \ CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or n \ ame HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through 346 or (r \ esid 347 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name \ HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or na \ me HH11 or name HH12)) or resid 348 through 457)) selection = (chain 'K' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 233 or (resid 234 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name OE1 o \ r name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3) \ ) or resid 235 through 457)) selection = (chain 'L' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 233 or (resid 234 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name OE1 o \ r name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3) \ ) or resid 235 through 254 or (resid 255 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ3)) or resid 256 through 340 or (resid 341 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2 or name HA or \ name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG22 or nam \ e HG23)) or resid 342 through 346 or (resid 347 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 348 throu \ gh 457)) } ncs_group { reference = chain 'M' selection = chain 'N' } 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: 0.760 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: 0.710 Extract box with map and model: 6.190 Check model and map are aligned: 0.720 Set scattering table: 0.450 Process input model: 149.680 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5820 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 : 0.005 0.176 34186 Z= 0.322 Angle : 0.725 9.735 46208 Z= 0.429 Chirality : 0.041 0.178 4886 Planarity : 0.005 0.089 5980 Dihedral : 13.560 87.976 13056 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.97 % Rotamer: Outliers : 1.90 % Allowed : 7.52 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.12), residues: 4000 helix: 0.08 (0.11), residues: 1716 sheet: 0.45 (0.23), residues: 520 loop : -0.48 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 306 HIS 0.008 0.001 HIS K 407 PHE 0.030 0.002 PHE E 252 TYR 0.022 0.002 TYR N 308 ARG 0.013 0.001 ARG K 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 906 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 837 time to evaluate : 4.067 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.7999 (mt) cc_final: 0.7504 (tp) REVERT: C 230 VAL cc_start: 0.8309 (m) cc_final: 0.8083 (p) REVERT: C 286 LEU cc_start: 0.8207 (mt) cc_final: 0.7963 (mt) REVERT: C 297 MET cc_start: 0.8088 (ptm) cc_final: 0.7696 (ptm) REVERT: C 388 LEU cc_start: 0.8598 (tp) cc_final: 0.8156 (tt) REVERT: G 177 LEU cc_start: 0.6369 (mt) cc_final: 0.6155 (mp) REVERT: G 297 MET cc_start: 0.3298 (tmt) cc_final: 0.2509 (ppp) REVERT: I 388 LEU cc_start: 0.8645 (tp) cc_final: 0.8413 (tt) REVERT: M 58 LEU cc_start: 0.4785 (mt) cc_final: 0.4485 (mt) REVERT: N 304 ILE cc_start: 0.8791 (mt) cc_final: 0.8294 (mm) outliers start: 69 outliers final: 26 residues processed: 897 average time/residue: 0.9935 time to fit residues: 1371.4001 Evaluate side-chains 543 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 517 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 10.0000 chunk 303 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 103 optimal weight: 0.0050 chunk 204 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 313 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 190 optimal weight: 9.9990 chunk 233 optimal weight: 2.9990 chunk 363 optimal weight: 6.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 228 ASN B 231 GLN B 234 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN G 264 GLN G 383 GLN ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 279 ASN ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 279 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 34186 Z= 0.223 Angle : 0.552 7.891 46208 Z= 0.296 Chirality : 0.038 0.152 4886 Planarity : 0.004 0.058 5980 Dihedral : 5.997 47.853 4644 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.02 % Rotamer: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.13), residues: 4000 helix: 1.30 (0.12), residues: 1692 sheet: 0.55 (0.23), residues: 520 loop : -0.39 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 306 HIS 0.016 0.002 HIS K 407 PHE 0.042 0.002 PHE K 442 TYR 0.021 0.001 TYR M 123 ARG 0.009 0.001 ARG G 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 592 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 591 time to evaluate : 4.072 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 ILE cc_start: 0.8500 (pt) cc_final: 0.8256 (mt) REVERT: B 346 LEU cc_start: 0.7840 (tp) cc_final: 0.7329 (tt) REVERT: C 293 VAL cc_start: 0.8840 (t) cc_final: 0.8620 (t) REVERT: C 297 MET cc_start: 0.8230 (ptm) cc_final: 0.7627 (ptm) REVERT: C 388 LEU cc_start: 0.8559 (tp) cc_final: 0.8332 (tt) REVERT: G 177 LEU cc_start: 0.6558 (mt) cc_final: 0.6351 (mp) REVERT: I 286 LEU cc_start: 0.8099 (mt) cc_final: 0.7880 (mt) REVERT: I 388 LEU cc_start: 0.8440 (tp) cc_final: 0.8225 (tt) REVERT: L 222 LYS cc_start: 0.5391 (tptp) cc_final: 0.4982 (mptt) REVERT: M 131 CYS cc_start: 0.8275 (m) cc_final: 0.7813 (m) REVERT: N 131 CYS cc_start: 0.8340 (m) cc_final: 0.7926 (m) outliers start: 1 outliers final: 1 residues processed: 592 average time/residue: 1.0235 time to fit residues: 941.5900 Evaluate side-chains 474 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 473 time to evaluate : 4.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 302 optimal weight: 8.9990 chunk 247 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 363 optimal weight: 9.9990 chunk 393 optimal weight: 0.8980 chunk 324 optimal weight: 10.0000 chunk 360 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 291 optimal weight: 20.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN C 243 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 GLN L 449 GLN ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 34186 Z= 0.288 Angle : 0.584 7.747 46208 Z= 0.317 Chirality : 0.038 0.231 4886 Planarity : 0.004 0.054 5980 Dihedral : 6.277 58.060 4644 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.13), residues: 4000 helix: 1.16 (0.12), residues: 1694 sheet: 0.57 (0.23), residues: 518 loop : -0.51 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 306 HIS 0.009 0.002 HIS K 407 PHE 0.032 0.002 PHE F 350 TYR 0.031 0.002 TYR M 163 ARG 0.015 0.001 ARG K 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 523 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 522 time to evaluate : 5.205 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 LEU cc_start: 0.8065 (tp) cc_final: 0.7610 (tt) REVERT: C 297 MET cc_start: 0.8699 (ptm) cc_final: 0.8259 (ptm) REVERT: C 385 MET cc_start: 0.8231 (ptp) cc_final: 0.7784 (ptm) REVERT: D 297 MET cc_start: 0.7771 (ptm) cc_final: 0.7162 (ptp) REVERT: L 222 LYS cc_start: 0.5375 (tptp) cc_final: 0.5079 (mptt) REVERT: M 131 CYS cc_start: 0.8519 (m) cc_final: 0.8043 (m) REVERT: N 131 CYS cc_start: 0.8359 (m) cc_final: 0.7963 (m) outliers start: 1 outliers final: 1 residues processed: 523 average time/residue: 1.0661 time to fit residues: 862.7722 Evaluate side-chains 438 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 437 time to evaluate : 4.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 359 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 188 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 365 optimal weight: 6.9990 chunk 386 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 346 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN B 386 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** I 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 146 HIS ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.184 34186 Z= 0.332 Angle : 0.626 8.287 46208 Z= 0.342 Chirality : 0.039 0.176 4886 Planarity : 0.005 0.069 5980 Dihedral : 6.569 58.497 4644 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.12), residues: 4000 helix: 0.50 (0.12), residues: 1750 sheet: 0.25 (0.23), residues: 510 loop : -0.88 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 306 HIS 0.007 0.002 HIS I 299 PHE 0.045 0.002 PHE F 259 TYR 0.026 0.002 TYR F 238 ARG 0.006 0.001 ARG I 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 472 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 471 time to evaluate : 4.031 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 297 MET cc_start: 0.8832 (ptm) cc_final: 0.8410 (ptm) REVERT: C 388 LEU cc_start: 0.8673 (tp) cc_final: 0.8370 (tt) REVERT: D 278 ILE cc_start: 0.6739 (mp) cc_final: 0.5934 (mp) REVERT: D 297 MET cc_start: 0.7973 (ptm) cc_final: 0.7468 (ptm) REVERT: F 286 LEU cc_start: 0.6706 (tt) cc_final: 0.6367 (tt) REVERT: J 278 ILE cc_start: 0.7018 (mp) cc_final: 0.6598 (mp) REVERT: J 297 MET cc_start: 0.7665 (ptm) cc_final: 0.7403 (ptm) REVERT: M 58 LEU cc_start: 0.5328 (mt) cc_final: 0.5092 (mt) REVERT: M 131 CYS cc_start: 0.8572 (m) cc_final: 0.8161 (m) REVERT: M 153 GLU cc_start: 0.8393 (pm20) cc_final: 0.8124 (pm20) REVERT: M 159 MET cc_start: 0.7321 (mmm) cc_final: 0.6920 (mmm) REVERT: N 131 CYS cc_start: 0.8530 (m) cc_final: 0.8159 (m) outliers start: 1 outliers final: 1 residues processed: 472 average time/residue: 0.9601 time to fit residues: 701.1161 Evaluate side-chains 394 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 3.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 322 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 287 optimal weight: 8.9990 chunk 159 optimal weight: 0.4980 chunk 329 optimal weight: 7.9990 chunk 267 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 197 optimal weight: 7.9990 chunk 347 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN B 269 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34186 Z= 0.213 Angle : 0.524 7.532 46208 Z= 0.281 Chirality : 0.038 0.150 4886 Planarity : 0.004 0.062 5980 Dihedral : 6.132 65.578 4644 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.03 % Allowed : 1.43 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.13), residues: 4000 helix: 0.86 (0.12), residues: 1736 sheet: 0.13 (0.22), residues: 554 loop : -0.72 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 424 HIS 0.009 0.001 HIS B 233 PHE 0.025 0.002 PHE I 232 TYR 0.020 0.001 TYR M 163 ARG 0.005 0.000 ARG I 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 453 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 452 time to evaluate : 4.061 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 LEU cc_start: 0.8032 (tp) cc_final: 0.7781 (tt) REVERT: C 297 MET cc_start: 0.8695 (ptm) cc_final: 0.8279 (ptm) REVERT: F 286 LEU cc_start: 0.6409 (tt) cc_final: 0.6059 (tt) REVERT: H 295 MET cc_start: 0.5413 (mmm) cc_final: 0.5090 (mmm) REVERT: J 297 MET cc_start: 0.7594 (ptm) cc_final: 0.7347 (ptm) REVERT: M 131 CYS cc_start: 0.8392 (m) cc_final: 0.8004 (m) REVERT: M 159 MET cc_start: 0.7274 (mmm) cc_final: 0.6962 (mmm) REVERT: N 131 CYS cc_start: 0.8430 (m) cc_final: 0.8042 (m) outliers start: 1 outliers final: 1 residues processed: 453 average time/residue: 0.9490 time to fit residues: 667.7104 Evaluate side-chains 389 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 388 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 2.9990 chunk 348 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 387 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 128 optimal weight: 0.0670 chunk 203 optimal weight: 10.0000 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN B 269 GLN D 234 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN I 233 HIS ** K 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34186 Z= 0.165 Angle : 0.483 6.819 46208 Z= 0.256 Chirality : 0.038 0.143 4886 Planarity : 0.004 0.063 5980 Dihedral : 5.812 66.454 4644 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.13), residues: 4000 helix: 1.14 (0.12), residues: 1742 sheet: 0.18 (0.22), residues: 542 loop : -0.53 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 424 HIS 0.007 0.001 HIS N 237 PHE 0.022 0.001 PHE F 241 TYR 0.022 0.001 TYR F 238 ARG 0.004 0.000 ARG I 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 439 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 4.118 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 297 MET cc_start: 0.8656 (ptm) cc_final: 0.8255 (ptm) REVERT: F 286 LEU cc_start: 0.6086 (tt) cc_final: 0.5772 (tt) REVERT: J 297 MET cc_start: 0.7461 (ptm) cc_final: 0.7234 (ptm) REVERT: M 14 MET cc_start: 0.6166 (mmp) cc_final: 0.5922 (mmp) REVERT: M 131 CYS cc_start: 0.8371 (m) cc_final: 0.7923 (m) REVERT: N 131 CYS cc_start: 0.8417 (m) cc_final: 0.7980 (m) REVERT: N 243 GLN cc_start: 0.8246 (mp10) cc_final: 0.8001 (mp10) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.9312 time to fit residues: 637.2021 Evaluate side-chains 384 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 373 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 282 optimal weight: 30.0000 chunk 218 optimal weight: 2.9990 chunk 325 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 385 optimal weight: 4.9990 chunk 241 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** I 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 453 ASN ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** N 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.6212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34186 Z= 0.240 Angle : 0.537 6.606 46208 Z= 0.291 Chirality : 0.038 0.170 4886 Planarity : 0.004 0.069 5980 Dihedral : 5.955 60.865 4644 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.13), residues: 4000 helix: 0.96 (0.12), residues: 1724 sheet: -0.07 (0.22), residues: 580 loop : -0.72 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 306 HIS 0.021 0.002 HIS M 237 PHE 0.023 0.002 PHE F 241 TYR 0.021 0.002 TYR I 260 ARG 0.011 0.001 ARG N 172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 417 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 4.723 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 297 MET cc_start: 0.8710 (ptm) cc_final: 0.8310 (ptm) REVERT: C 385 MET cc_start: 0.8287 (ptm) cc_final: 0.8039 (ptm) REVERT: F 286 LEU cc_start: 0.6159 (tt) cc_final: 0.5804 (tt) REVERT: J 297 MET cc_start: 0.7650 (ptm) cc_final: 0.7239 (ptm) REVERT: M 131 CYS cc_start: 0.8497 (m) cc_final: 0.8145 (m) REVERT: M 159 MET cc_start: 0.7226 (mmm) cc_final: 0.6827 (mmm) REVERT: N 131 CYS cc_start: 0.8392 (m) cc_final: 0.7964 (m) REVERT: N 243 GLN cc_start: 0.8293 (mp10) cc_final: 0.8002 (mp10) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.9381 time to fit residues: 611.5808 Evaluate side-chains 366 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 4.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 238 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 230 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 chunk 262 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 GLN H 228 ASN H 366 ASN ** I 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 34186 Z= 0.348 Angle : 0.645 7.462 46208 Z= 0.356 Chirality : 0.039 0.293 4886 Planarity : 0.005 0.099 5980 Dihedral : 6.462 61.929 4644 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4000 helix: 0.16 (0.12), residues: 1762 sheet: -0.53 (0.22), residues: 552 loop : -1.09 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 294 HIS 0.011 0.002 HIS B 233 PHE 0.040 0.003 PHE K 377 TYR 0.026 0.002 TYR E 344 ARG 0.022 0.001 ARG J 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 387 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 4.226 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 297 MET cc_start: 0.8707 (ptm) cc_final: 0.8157 (ptm) REVERT: F 286 LEU cc_start: 0.6606 (tt) cc_final: 0.6251 (tt) REVERT: H 295 MET cc_start: 0.5583 (mmm) cc_final: 0.5216 (mmm) REVERT: J 297 MET cc_start: 0.7915 (ptm) cc_final: 0.7615 (ptm) REVERT: M 131 CYS cc_start: 0.8606 (m) cc_final: 0.8241 (m) REVERT: M 243 GLN cc_start: 0.8476 (mp10) cc_final: 0.8176 (mp10) REVERT: N 131 CYS cc_start: 0.8828 (m) cc_final: 0.8491 (m) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.9425 time to fit residues: 573.0130 Evaluate side-chains 328 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 4.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 350 optimal weight: 9.9990 chunk 369 optimal weight: 7.9990 chunk 336 optimal weight: 3.9990 chunk 359 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 chunk 282 optimal weight: 0.2980 chunk 110 optimal weight: 20.0000 chunk 324 optimal weight: 8.9990 chunk 339 optimal weight: 10.0000 chunk 358 optimal weight: 5.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN B 265 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** I 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.7129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34186 Z= 0.218 Angle : 0.537 7.645 46208 Z= 0.288 Chirality : 0.038 0.151 4886 Planarity : 0.004 0.073 5980 Dihedral : 6.064 67.876 4644 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 4000 helix: 0.52 (0.12), residues: 1726 sheet: -0.49 (0.22), residues: 542 loop : -0.92 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 424 HIS 0.009 0.001 HIS B 233 PHE 0.029 0.002 PHE L 350 TYR 0.021 0.002 TYR M 163 ARG 0.015 0.001 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 389 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 4.156 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 297 MET cc_start: 0.8605 (ptm) cc_final: 0.8175 (ptm) REVERT: C 388 LEU cc_start: 0.8682 (tp) cc_final: 0.8454 (tt) REVERT: F 286 LEU cc_start: 0.6596 (tt) cc_final: 0.6238 (tt) REVERT: J 297 MET cc_start: 0.7840 (ptm) cc_final: 0.7534 (ptm) REVERT: M 131 CYS cc_start: 0.8602 (m) cc_final: 0.8200 (m) REVERT: M 159 MET cc_start: 0.7362 (mmm) cc_final: 0.6963 (mmm) REVERT: M 243 GLN cc_start: 0.8307 (mp10) cc_final: 0.7910 (mp10) REVERT: N 131 CYS cc_start: 0.8653 (m) cc_final: 0.8270 (m) REVERT: N 243 GLN cc_start: 0.8274 (mp10) cc_final: 0.7938 (mp10) outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.9359 time to fit residues: 574.8407 Evaluate side-chains 329 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 4.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 235 optimal weight: 9.9990 chunk 379 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 180 optimal weight: 0.4980 chunk 264 optimal weight: 4.9990 chunk 398 optimal weight: 7.9990 chunk 366 optimal weight: 3.9990 chunk 317 optimal weight: 8.9990 chunk 32 optimal weight: 0.0000 chunk 245 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 overall best weight: 3.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN D 234 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** I 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.7230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34186 Z= 0.175 Angle : 0.497 6.407 46208 Z= 0.264 Chirality : 0.038 0.158 4886 Planarity : 0.004 0.071 5980 Dihedral : 5.684 67.283 4644 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 4000 helix: 0.87 (0.12), residues: 1724 sheet: -0.38 (0.22), residues: 522 loop : -0.77 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 424 HIS 0.011 0.001 HIS C 233 PHE 0.023 0.001 PHE K 442 TYR 0.023 0.001 TYR M 163 ARG 0.007 0.001 ARG D 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 391 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 4.103 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 286 LEU cc_start: 0.6562 (tt) cc_final: 0.6164 (tt) REVERT: G 443 ASP cc_start: 0.7844 (p0) cc_final: 0.7632 (p0) REVERT: J 297 MET cc_start: 0.7698 (ptm) cc_final: 0.7359 (ptm) REVERT: M 131 CYS cc_start: 0.8482 (m) cc_final: 0.8145 (m) REVERT: M 243 GLN cc_start: 0.8328 (mp10) cc_final: 0.7926 (mp10) REVERT: N 131 CYS cc_start: 0.8301 (m) cc_final: 0.7928 (m) REVERT: N 243 GLN cc_start: 0.8245 (mp10) cc_final: 0.7923 (mp10) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.9356 time to fit residues: 575.9543 Evaluate side-chains 337 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 4.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 252 optimal weight: 10.0000 chunk 338 optimal weight: 30.0000 chunk 97 optimal weight: 6.9990 chunk 292 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 326 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** G 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** I 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.052641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.041988 restraints weight = 920392.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.043726 restraints weight = 563041.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.044966 restraints weight = 378868.765| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.7806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 34186 Z= 0.358 Angle : 0.651 8.240 46208 Z= 0.359 Chirality : 0.039 0.153 4886 Planarity : 0.005 0.086 5980 Dihedral : 6.370 62.946 4644 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 26.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.13), residues: 4000 helix: 0.10 (0.12), residues: 1730 sheet: -0.87 (0.21), residues: 582 loop : -1.10 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 424 HIS 0.011 0.002 HIS L 233 PHE 0.032 0.003 PHE M 166 TYR 0.025 0.002 TYR M 163 ARG 0.010 0.001 ARG J 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12589.20 seconds wall clock time: 219 minutes 59.39 seconds (13199.39 seconds total)