Starting phenix.real_space_refine on Sun Dec 10 04:59:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsr_32114/12_2023/7vsr_32114_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsr_32114/12_2023/7vsr_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_32114/12_2023/7vsr_32114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsr_32114/12_2023/7vsr_32114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsr_32114/12_2023/7vsr_32114_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsr_32114/12_2023/7vsr_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 21.40, per 1000 atoms: 0.32 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: 43.14 Conformation dependent library (CDL) restraints added in 5.1 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: 7.33 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: 25.33 Time building geometry restraints manager: 45.56 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: 28093 17.60 - 35.19: 2193 35.19 - 52.79: 402 52.79 - 70.38: 67 70.38 - 87.98: 15 Dihedral angle restraints: 30770 sinusoidal: 16412 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 30767 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: 0.920 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: 6.430 Check model and map are aligned: 0.750 Set scattering table: 0.470 Process input model: 171.090 Find NCS groups from input model: 2.940 Set up NCS constraints: 0.220 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.130 ------------------------------------------------------------------------------- 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 : 4.230 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 outliers start: 69 outliers final: 26 residues processed: 897 average time/residue: 1.0277 time to fit residues: 1424.1277 Evaluate side-chains 540 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 514 time to evaluate : 4.547 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 4 residues processed: 26 average time/residue: 0.8117 time to fit residues: 40.1441 ------------------------------------------------------------------------------- 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: 9.9990 chunk 303 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 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: 10.0000 chunk 233 optimal weight: 2.9990 chunk 363 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 449 GLN ** M 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 279 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34186 Z= 0.262 Angle : 0.585 8.187 46208 Z= 0.316 Chirality : 0.038 0.157 4886 Planarity : 0.004 0.056 5980 Dihedral : 6.168 50.177 4644 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.11 % Allowed : 2.34 % Favored : 97.55 % 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: 0.56 (0.13), residues: 4000 helix: 1.27 (0.12), residues: 1666 sheet: 0.55 (0.23), residues: 516 loop : -0.47 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 306 HIS 0.015 0.002 HIS K 407 PHE 0.047 0.002 PHE K 442 TYR 0.022 0.002 TYR I 260 ARG 0.011 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 575 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 571 time to evaluate : 4.322 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 outliers start: 4 outliers final: 2 residues processed: 575 average time/residue: 0.9948 time to fit residues: 873.5556 Evaluate side-chains 472 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 470 time to evaluate : 4.189 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.5882 time to fit residues: 7.4237 ------------------------------------------------------------------------------- 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: 0.9990 chunk 112 optimal weight: 2.9990 chunk 302 optimal weight: 0.7980 chunk 247 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 363 optimal weight: 10.0000 chunk 393 optimal weight: 6.9990 chunk 324 optimal weight: 9.9990 chunk 360 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 291 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 383 GLN ** M 155 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 34186 Z= 0.203 Angle : 0.515 7.231 46208 Z= 0.275 Chirality : 0.038 0.169 4886 Planarity : 0.004 0.054 5980 Dihedral : 6.041 57.244 4644 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.06 % Allowed : 1.49 % Favored : 98.46 % 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: 0.73 (0.13), residues: 4000 helix: 1.46 (0.12), residues: 1668 sheet: 0.65 (0.23), residues: 516 loop : -0.45 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 424 HIS 0.009 0.001 HIS H 233 PHE 0.026 0.002 PHE F 350 TYR 0.028 0.001 TYR M 163 ARG 0.013 0.000 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 540 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 538 time to evaluate : 4.321 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 outliers start: 2 outliers final: 2 residues processed: 540 average time/residue: 1.0150 time to fit residues: 844.6542 Evaluate side-chains 440 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 438 time to evaluate : 4.201 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5721 time to fit residues: 7.3406 ------------------------------------------------------------------------------- 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: 0.9990 chunk 188 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 365 optimal weight: 10.0000 chunk 386 optimal weight: 8.9990 chunk 190 optimal weight: 4.9990 chunk 346 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34186 Z= 0.225 Angle : 0.536 11.755 46208 Z= 0.285 Chirality : 0.038 0.163 4886 Planarity : 0.004 0.073 5980 Dihedral : 6.017 56.732 4644 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 0.68 (0.13), residues: 4000 helix: 1.36 (0.12), residues: 1698 sheet: 0.57 (0.23), residues: 494 loop : -0.41 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 424 HIS 0.007 0.001 HIS K 407 PHE 0.045 0.002 PHE I 232 TYR 0.019 0.001 TYR M 163 ARG 0.008 0.001 ARG I 349 *********************** 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 492 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 4.336 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 outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.9730 time to fit residues: 734.7217 Evaluate side-chains 417 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 4.178 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0749 ------------------------------------------------------------------------------- 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: 6.9990 chunk 219 optimal weight: 0.0670 chunk 5 optimal weight: 9.9990 chunk 287 optimal weight: 20.0000 chunk 159 optimal weight: 30.0000 chunk 329 optimal weight: 5.9990 chunk 267 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 347 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 overall best weight: 6.0126 ------------------------------------------------------------------------------- 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** B 228 ASN B 389 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 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 237 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 34186 Z= 0.247 Angle : 0.546 6.949 46208 Z= 0.293 Chirality : 0.038 0.196 4886 Planarity : 0.004 0.072 5980 Dihedral : 6.073 58.729 4644 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % 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: 0.33 (0.13), residues: 4000 helix: 1.06 (0.12), residues: 1734 sheet: 0.29 (0.22), residues: 524 loop : -0.60 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 306 HIS 0.009 0.001 HIS B 233 PHE 0.048 0.002 PHE I 232 TYR 0.023 0.002 TYR M 163 ARG 0.014 0.001 ARG C 283 *********************** 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 461 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 461 time to evaluate : 4.313 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 outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.9577 time to fit residues: 688.0811 Evaluate side-chains 396 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 4.283 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2781 ------------------------------------------------------------------------------- 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: 0.8980 chunk 348 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 387 optimal weight: 10.0000 chunk 321 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 128 optimal weight: 0.1980 chunk 203 optimal weight: 9.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- 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** 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** H 228 ASN ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34186 Z= 0.178 Angle : 0.488 6.734 46208 Z= 0.258 Chirality : 0.037 0.142 4886 Planarity : 0.004 0.065 5980 Dihedral : 5.771 60.846 4644 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: 0.48 (0.13), residues: 4000 helix: 1.20 (0.12), residues: 1738 sheet: 0.28 (0.22), residues: 536 loop : -0.52 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 294 HIS 0.007 0.001 HIS K 233 PHE 0.024 0.001 PHE I 232 TYR 0.021 0.001 TYR M 163 ARG 0.003 0.000 ARG D 337 *********************** 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 445 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 4.290 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 outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.9482 time to fit residues: 659.6966 Evaluate side-chains 379 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 4.208 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1810 ------------------------------------------------------------------------------- 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: 0.8980 chunk 220 optimal weight: 9.9990 chunk 282 optimal weight: 30.0000 chunk 218 optimal weight: 3.9990 chunk 325 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 385 optimal weight: 0.0770 chunk 241 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 overall best weight: 3.9944 ------------------------------------------------------------------------------- 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** B 228 ASN B 386 ASN C 234 GLN D 234 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** K 407 HIS ** 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 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: 0.6267 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 34186 Z= 0.183 Angle : 0.487 6.507 46208 Z= 0.259 Chirality : 0.037 0.144 4886 Planarity : 0.004 0.070 5980 Dihedral : 5.698 59.197 4644 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 0.50 (0.13), residues: 4000 helix: 1.28 (0.12), residues: 1724 sheet: 0.33 (0.22), residues: 532 loop : -0.57 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 424 HIS 0.011 0.001 HIS M 237 PHE 0.044 0.002 PHE I 232 TYR 0.027 0.001 TYR F 238 ARG 0.003 0.000 ARG C 283 *********************** 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 440 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 440 time to evaluate : 4.238 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 outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.9582 time to fit residues: 663.3126 Evaluate side-chains 378 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 4.203 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2018 ------------------------------------------------------------------------------- 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: 9.9990 chunk 153 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 245 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 303 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN C 234 GLN C 243 GLN D 231 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN ** 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** ** J 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 448 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 34186 Z= 0.308 Angle : 0.609 6.807 46208 Z= 0.335 Chirality : 0.039 0.147 4886 Planarity : 0.005 0.063 5980 Dihedral : 6.273 58.503 4644 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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 (0.13), residues: 4000 helix: 0.55 (0.12), residues: 1750 sheet: -0.17 (0.22), residues: 572 loop : -0.86 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 306 HIS 0.013 0.002 HIS M 237 PHE 0.033 0.002 PHE K 377 TYR 0.023 0.002 TYR I 260 ARG 0.008 0.001 ARG K 348 *********************** 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 413 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 4.296 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 outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.9764 time to fit residues: 625.8443 Evaluate side-chains 351 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 4.223 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2568 ------------------------------------------------------------------------------- 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: 10.0000 chunk 369 optimal weight: 7.9990 chunk 336 optimal weight: 5.9990 chunk 359 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 282 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 324 optimal weight: 8.9990 chunk 339 optimal weight: 5.9990 chunk 358 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- 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** 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** ** J 231 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 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: 0.6468 moved from start: 0.6964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34186 Z= 0.290 Angle : 0.591 7.054 46208 Z= 0.322 Chirality : 0.039 0.153 4886 Planarity : 0.005 0.069 5980 Dihedral : 6.185 58.784 4644 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -0.60 (0.13), residues: 4000 helix: 0.25 (0.12), residues: 1762 sheet: -0.52 (0.22), residues: 570 loop : -0.95 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 306 HIS 0.012 0.002 HIS C 233 PHE 0.043 0.002 PHE I 232 TYR 0.023 0.002 TYR M 163 ARG 0.012 0.001 ARG N 172 *********************** 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 399 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 4.276 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 outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.9617 time to fit residues: 600.6530 Evaluate side-chains 340 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 4.256 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1424 ------------------------------------------------------------------------------- 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: 10.0000 chunk 379 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 398 optimal weight: 10.0000 chunk 366 optimal weight: 6.9990 chunk 317 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 245 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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** B 228 ASN C 264 GLN 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** ** J 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 423 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.7405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 34186 Z= 0.303 Angle : 0.611 7.451 46208 Z= 0.334 Chirality : 0.039 0.169 4886 Planarity : 0.005 0.069 5980 Dihedral : 6.301 59.947 4644 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -0.86 (0.13), residues: 4000 helix: 0.08 (0.12), residues: 1752 sheet: -0.79 (0.22), residues: 546 loop : -1.08 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 306 HIS 0.007 0.002 HIS K 233 PHE 0.029 0.002 PHE D 232 TYR 0.025 0.002 TYR M 163 ARG 0.014 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 370 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 4.229 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 outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.9494 time to fit residues: 546.4948 Evaluate side-chains 311 residues out of total 3630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 4.222 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1001 ------------------------------------------------------------------------------- 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: 10.0000 chunk 97 optimal weight: 3.9990 chunk 292 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 317 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 326 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- 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** B 228 ASN B 269 GLN D 234 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** I 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 231 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.053855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.042620 restraints weight = 864548.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.044457 restraints weight = 525972.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.045766 restraints weight = 352506.377| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.7644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 34186 Z= 0.243 Angle : 0.558 8.402 46208 Z= 0.301 Chirality : 0.038 0.155 4886 Planarity : 0.004 0.072 5980 Dihedral : 6.017 59.198 4644 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % 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: -0.68 (0.13), residues: 4000 helix: 0.25 (0.12), residues: 1738 sheet: -0.75 (0.22), residues: 550 loop : -0.97 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 424 HIS 0.007 0.001 HIS K 233 PHE 0.026 0.002 PHE F 241 TYR 0.026 0.002 TYR M 163 ARG 0.009 0.001 ARG D 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12856.05 seconds wall clock time: 225 minutes 3.70 seconds (13503.70 seconds total)