Starting phenix.real_space_refine on Sun Feb 18 12:38:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/02_2024/6vfx_21194_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/02_2024/6vfx_21194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/02_2024/6vfx_21194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/02_2024/6vfx_21194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/02_2024/6vfx_21194_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/02_2024/6vfx_21194_trim_updated.pdb" } resolution = 2.9 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= 0.001 sd= 0.120 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 17 5.49 5 Mg 5 5.21 5 S 154 5.16 5 C 23050 2.51 5 N 6213 2.21 5 O 7013 1.98 5 H 36896 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 73348 Number of models: 1 Model: "" Number of chains: 27 Chain: "C" Number of atoms: 5207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5207 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 13, 'TRANS': 319} Chain breaks: 3 Chain: "B" Number of atoms: 5283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5283 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 14, 'TRANS': 322} Chain breaks: 2 Chain: "E" Number of atoms: 5357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 5357 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain breaks: 2 Chain: "F" Number of atoms: 5038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 5038 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain breaks: 3 Chain: "D" Number of atoms: 5314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5314 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 13, 'TRANS': 325} Chain breaks: 2 Chain: "A" Number of atoms: 5311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5311 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 14, 'TRANS': 325} Chain breaks: 2 Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 34 Classifications: {'peptide': 7} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "O" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "P" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "Q" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "R" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "S" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "T" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "U" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "H" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2968 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 1 Chain: "I" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 2982 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain breaks: 1 Chain: "J" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "K" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3007 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 7, 'TRANS': 185} Chain: "M" Number of atoms: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2910 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 7, 'TRANS': 178} Chain breaks: 1 Chain: "N" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 2975 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.73, per 1000 atoms: 0.32 Number of scatterers: 73348 At special positions: 0 Unit cell: (132.5, 146.28, 183.38, 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 17 15.00 Mg 5 11.99 O 7013 8.00 N 6213 7.00 C 23050 6.00 H 36896 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: 49.26 Conformation dependent library (CDL) restraints added in 6.0 seconds 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8620 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 206 helices and 59 sheets defined 45.4% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.05 Creating SS restraints... Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 82 through 99 Processing helix chain 'C' and resid 125 through 134 removed outlier: 3.641A pdb=" N ARG C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 158 through 169 removed outlier: 3.521A pdb=" N ILE C 162 " --> pdb=" O GLU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 178 removed outlier: 4.100A pdb=" N ARG C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 189 removed outlier: 3.692A pdb=" N ILE C 189 " --> pdb=" O ILE C 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 186 through 189' Processing helix chain 'C' and resid 205 through 215 removed outlier: 4.331A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 282 through 288 removed outlier: 3.704A pdb=" N ILE C 288 " --> pdb=" O LYS C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 297 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 320 through 324 Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.544A pdb=" N ALA C 358 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 386 removed outlier: 3.566A pdb=" N VAL C 375 " --> pdb=" O ARG C 372 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 377 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU C 380 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR C 384 " --> pdb=" O ASP C 381 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 386 " --> pdb=" O MET C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 403 Processing helix chain 'B' and resid 67 through 74 Processing helix chain 'B' and resid 82 through 100 Processing helix chain 'B' and resid 125 through 134 removed outlier: 3.737A pdb=" N ARG B 134 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.658A pdb=" N LYS B 168 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 178 removed outlier: 4.093A pdb=" N ARG B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 189 removed outlier: 3.694A pdb=" N ILE B 189 " --> pdb=" O ILE B 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 186 through 189' Processing helix chain 'B' and resid 205 through 215 removed outlier: 4.476A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.846A pdb=" N GLU B 255 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 256 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 258 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 288 removed outlier: 3.545A pdb=" N ILE B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 297 Processing helix chain 'B' and resid 301 through 304 No H-bonds generated for 'chain 'B' and resid 301 through 304' Processing helix chain 'B' and resid 318 through 325 removed outlier: 3.675A pdb=" N ILE B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 351 through 364 removed outlier: 3.697A pdb=" N GLU B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 378 removed outlier: 3.639A pdb=" N ARG B 372 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU B 376 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS B 378 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 386 Processing helix chain 'B' and resid 400 through 403 No H-bonds generated for 'chain 'B' and resid 400 through 403' Processing helix chain 'E' and resid 67 through 75 Processing helix chain 'E' and resid 82 through 99 Processing helix chain 'E' and resid 125 through 135 removed outlier: 3.589A pdb=" N ARG E 134 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 147 No H-bonds generated for 'chain 'E' and resid 145 through 147' Processing helix chain 'E' and resid 158 through 169 Processing helix chain 'E' and resid 173 through 178 removed outlier: 4.126A pdb=" N ARG E 178 " --> pdb=" O GLU E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 189 removed outlier: 3.744A pdb=" N ILE E 189 " --> pdb=" O ILE E 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 186 through 189' Processing helix chain 'E' and resid 205 through 215 removed outlier: 4.289A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 262 removed outlier: 3.909A pdb=" N GLU E 255 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS E 256 " --> pdb=" O GLY E 253 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR E 262 " --> pdb=" O ARG E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 288 removed outlier: 3.796A pdb=" N ILE E 288 " --> pdb=" O LYS E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 301 through 304 No H-bonds generated for 'chain 'E' and resid 301 through 304' Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'E' and resid 332 through 341 Processing helix chain 'E' and resid 351 through 363 Processing helix chain 'E' and resid 371 through 378 Processing helix chain 'E' and resid 380 through 385 removed outlier: 3.716A pdb=" N ARG E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 403 Processing helix chain 'F' and resid 67 through 74 removed outlier: 3.522A pdb=" N VAL F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 100 removed outlier: 3.929A pdb=" N ARG F 100 " --> pdb=" O TYR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 136 Processing helix chain 'F' and resid 145 through 147 No H-bonds generated for 'chain 'F' and resid 145 through 147' Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 160 through 169 removed outlier: 3.576A pdb=" N CYS F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 178 removed outlier: 4.312A pdb=" N ARG F 178 " --> pdb=" O GLU F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 Processing helix chain 'F' and resid 252 through 262 removed outlier: 4.232A pdb=" N GLU F 255 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS F 256 " --> pdb=" O GLY F 253 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN F 260 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 288 removed outlier: 3.565A pdb=" N ILE F 288 " --> pdb=" O LYS F 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 284 through 288' Processing helix chain 'F' and resid 291 through 297 Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 320 through 326 removed outlier: 3.511A pdb=" N LEU F 325 " --> pdb=" O LEU F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 341 Processing helix chain 'F' and resid 351 through 364 removed outlier: 3.646A pdb=" N ARG F 364 " --> pdb=" O GLN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 369 No H-bonds generated for 'chain 'F' and resid 367 through 369' Processing helix chain 'F' and resid 371 through 383 removed outlier: 4.267A pdb=" N ASP F 381 " --> pdb=" O ARG F 377 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N THR F 382 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 403 Processing helix chain 'D' and resid 67 through 74 Processing helix chain 'D' and resid 82 through 99 Processing helix chain 'D' and resid 125 through 135 removed outlier: 3.673A pdb=" N ARG D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 173 through 178 removed outlier: 4.054A pdb=" N ARG D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 189 removed outlier: 3.656A pdb=" N ILE D 189 " --> pdb=" O ILE D 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 186 through 189' Processing helix chain 'D' and resid 205 through 215 removed outlier: 4.404A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 262 removed outlier: 4.225A pdb=" N GLU D 255 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS D 256 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 288 removed outlier: 3.783A pdb=" N ILE D 288 " --> pdb=" O LYS D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 297 Processing helix chain 'D' and resid 301 through 304 No H-bonds generated for 'chain 'D' and resid 301 through 304' Processing helix chain 'D' and resid 320 through 325 removed outlier: 4.892A pdb=" N LEU D 325 " --> pdb=" O LEU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 342 Processing helix chain 'D' and resid 351 through 364 removed outlier: 3.543A pdb=" N GLU D 363 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 378 removed outlier: 3.648A pdb=" N ARG D 372 " --> pdb=" O ARG D 369 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 375 " --> pdb=" O ARG D 372 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N CYS D 378 " --> pdb=" O VAL D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 385 Processing helix chain 'D' and resid 399 through 403 Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 82 through 100 Processing helix chain 'A' and resid 102 through 105 Processing helix chain 'A' and resid 125 through 136 Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.181A pdb=" N ARG A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.610A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 282 through 288 Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 301 through 304 No H-bonds generated for 'chain 'A' and resid 301 through 304' Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'A' and resid 332 through 341 Processing helix chain 'A' and resid 351 through 364 Processing helix chain 'A' and resid 367 through 378 removed outlier: 3.961A pdb=" N SER A 373 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N CYS A 378 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 383 No H-bonds generated for 'chain 'A' and resid 380 through 383' Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'L' and resid 24 through 31 removed outlier: 3.580A pdb=" N GLU L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 58 Processing helix chain 'L' and resid 75 through 87 Processing helix chain 'L' and resid 103 through 109 Processing helix chain 'L' and resid 139 through 164 Processing helix chain 'L' and resid 168 through 174 Processing helix chain 'L' and resid 183 through 189 Processing helix chain 'O' and resid 24 through 31 removed outlier: 3.579A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 58 Processing helix chain 'O' and resid 75 through 87 Processing helix chain 'O' and resid 103 through 109 Processing helix chain 'O' and resid 139 through 164 Processing helix chain 'O' and resid 168 through 174 Processing helix chain 'O' and resid 183 through 189 Processing helix chain 'P' and resid 24 through 31 removed outlier: 3.580A pdb=" N GLU P 31 " --> pdb=" O ARG P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 58 Processing helix chain 'P' and resid 75 through 87 Processing helix chain 'P' and resid 103 through 109 Processing helix chain 'P' and resid 139 through 164 Processing helix chain 'P' and resid 168 through 174 Processing helix chain 'P' and resid 183 through 189 Processing helix chain 'Q' and resid 24 through 31 removed outlier: 3.579A pdb=" N GLU Q 31 " --> pdb=" O ARG Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 58 Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 103 through 109 Processing helix chain 'Q' and resid 139 through 164 Processing helix chain 'Q' and resid 168 through 174 Processing helix chain 'Q' and resid 183 through 189 Processing helix chain 'R' and resid 24 through 31 removed outlier: 3.579A pdb=" N GLU R 31 " --> pdb=" O ARG R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 58 Processing helix chain 'R' and resid 75 through 87 Processing helix chain 'R' and resid 103 through 109 Processing helix chain 'R' and resid 139 through 164 Processing helix chain 'R' and resid 168 through 174 Processing helix chain 'R' and resid 183 through 189 Processing helix chain 'S' and resid 24 through 31 removed outlier: 3.579A pdb=" N GLU S 31 " --> pdb=" O ARG S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 58 Processing helix chain 'S' and resid 75 through 87 Processing helix chain 'S' and resid 103 through 109 Processing helix chain 'S' and resid 139 through 164 Processing helix chain 'S' and resid 168 through 174 Processing helix chain 'S' and resid 183 through 189 Processing helix chain 'T' and resid 24 through 31 removed outlier: 3.579A pdb=" N GLU T 31 " --> pdb=" O ARG T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 58 Processing helix chain 'T' and resid 75 through 87 Processing helix chain 'T' and resid 103 through 109 Processing helix chain 'T' and resid 139 through 164 Processing helix chain 'T' and resid 168 through 174 Processing helix chain 'T' and resid 183 through 189 Processing helix chain 'U' and resid 24 through 31 removed outlier: 3.798A pdb=" N GLU U 31 " --> pdb=" O ARG U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 58 Processing helix chain 'U' and resid 75 through 87 Processing helix chain 'U' and resid 103 through 109 Processing helix chain 'U' and resid 139 through 164 Processing helix chain 'U' and resid 168 through 174 Processing helix chain 'U' and resid 183 through 189 Processing helix chain 'H' and resid 24 through 31 removed outlier: 3.595A pdb=" N GLU H 31 " --> pdb=" O ARG H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 58 Processing helix chain 'H' and resid 75 through 87 Processing helix chain 'H' and resid 103 through 109 Processing helix chain 'H' and resid 139 through 164 Processing helix chain 'H' and resid 168 through 174 Processing helix chain 'H' and resid 183 through 189 Processing helix chain 'I' and resid 24 through 31 removed outlier: 3.591A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 58 Processing helix chain 'I' and resid 75 through 87 Processing helix chain 'I' and resid 103 through 109 Processing helix chain 'I' and resid 139 through 164 Processing helix chain 'I' and resid 168 through 174 Processing helix chain 'I' and resid 183 through 189 Processing helix chain 'J' and resid 24 through 31 removed outlier: 3.613A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 58 Processing helix chain 'J' and resid 75 through 87 Processing helix chain 'J' and resid 103 through 109 Processing helix chain 'J' and resid 139 through 164 Processing helix chain 'J' and resid 168 through 174 Processing helix chain 'J' and resid 183 through 189 Processing helix chain 'K' and resid 24 through 31 removed outlier: 3.581A pdb=" N GLU K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 58 Processing helix chain 'K' and resid 75 through 87 Processing helix chain 'K' and resid 103 through 109 Processing helix chain 'K' and resid 139 through 164 Processing helix chain 'K' and resid 168 through 174 Processing helix chain 'K' and resid 183 through 189 Processing helix chain 'M' and resid 24 through 31 removed outlier: 3.581A pdb=" N GLU M 31 " --> pdb=" O ARG M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 75 through 87 Processing helix chain 'M' and resid 103 through 109 Processing helix chain 'M' and resid 139 through 164 Processing helix chain 'M' and resid 168 through 174 Processing helix chain 'M' and resid 183 through 189 Processing helix chain 'N' and resid 24 through 31 removed outlier: 3.633A pdb=" N GLU N 31 " --> pdb=" O ARG N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 58 Processing helix chain 'N' and resid 75 through 87 Processing helix chain 'N' and resid 103 through 109 Processing helix chain 'N' and resid 139 through 164 Processing helix chain 'N' and resid 168 through 174 Processing helix chain 'N' and resid 183 through 189 Processing sheet with id= A, first strand: chain 'C' and resid 309 through 313 removed outlier: 3.694A pdb=" N GLY C 119 " --> pdb=" O GLY C 249 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 219 through 222 Processing sheet with id= C, first strand: chain 'C' and resid 346 through 349 Processing sheet with id= D, first strand: chain 'B' and resid 309 through 313 removed outlier: 3.729A pdb=" N GLY B 119 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 219 through 222 Processing sheet with id= F, first strand: chain 'B' and resid 346 through 349 Processing sheet with id= G, first strand: chain 'E' and resid 309 through 312 Processing sheet with id= H, first strand: chain 'E' and resid 219 through 222 Processing sheet with id= I, first strand: chain 'E' and resid 346 through 349 Processing sheet with id= J, first strand: chain 'F' and resid 309 through 313 removed outlier: 3.555A pdb=" N VAL F 141 " --> pdb=" O ILE F 180 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 219 through 222 Processing sheet with id= L, first strand: chain 'F' and resid 346 through 349 removed outlier: 3.862A pdb=" N LYS F 394 " --> pdb=" O VAL F 411 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL F 411 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 309 through 312 Processing sheet with id= N, first strand: chain 'D' and resid 219 through 222 Processing sheet with id= O, first strand: chain 'D' and resid 346 through 349 Processing sheet with id= P, first strand: chain 'A' and resid 309 through 313 removed outlier: 3.697A pdb=" N GLY A 119 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 219 through 222 Processing sheet with id= R, first strand: chain 'A' and resid 346 through 349 Processing sheet with id= S, first strand: chain 'L' and resid 10 through 13 Processing sheet with id= T, first strand: chain 'L' and resid 33 through 37 removed outlier: 6.316A pdb=" N PHE L 65 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU L 36 " --> pdb=" O PHE L 65 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR L 67 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN L 194 " --> pdb=" O ALA L 118 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 99 through 101 removed outlier: 6.702A pdb=" N ARG L 123 " --> pdb=" O ALA L 100 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 10 through 13 Processing sheet with id= W, first strand: chain 'O' and resid 33 through 37 removed outlier: 6.315A pdb=" N PHE O 65 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU O 36 " --> pdb=" O PHE O 65 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR O 67 " --> pdb=" O LEU O 36 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN O 194 " --> pdb=" O ALA O 118 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'O' and resid 99 through 101 removed outlier: 6.701A pdb=" N ARG O 123 " --> pdb=" O ALA O 100 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'P' and resid 10 through 13 Processing sheet with id= Z, first strand: chain 'P' and resid 33 through 37 removed outlier: 6.316A pdb=" N PHE P 65 " --> pdb=" O VAL P 34 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU P 36 " --> pdb=" O PHE P 65 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR P 67 " --> pdb=" O LEU P 36 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN P 194 " --> pdb=" O ALA P 118 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'P' and resid 99 through 101 removed outlier: 6.702A pdb=" N ARG P 123 " --> pdb=" O ALA P 100 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Q' and resid 10 through 13 Processing sheet with id= AC, first strand: chain 'Q' and resid 33 through 37 removed outlier: 6.316A pdb=" N PHE Q 65 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU Q 36 " --> pdb=" O PHE Q 65 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR Q 67 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN Q 194 " --> pdb=" O ALA Q 118 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Q' and resid 99 through 101 removed outlier: 6.701A pdb=" N ARG Q 123 " --> pdb=" O ALA Q 100 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'R' and resid 10 through 13 Processing sheet with id= AF, first strand: chain 'R' and resid 33 through 37 removed outlier: 6.315A pdb=" N PHE R 65 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU R 36 " --> pdb=" O PHE R 65 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR R 67 " --> pdb=" O LEU R 36 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN R 194 " --> pdb=" O ALA R 118 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'R' and resid 99 through 101 removed outlier: 6.701A pdb=" N ARG R 123 " --> pdb=" O ALA R 100 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'S' and resid 10 through 13 Processing sheet with id= AI, first strand: chain 'S' and resid 33 through 37 removed outlier: 6.315A pdb=" N PHE S 65 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU S 36 " --> pdb=" O PHE S 65 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR S 67 " --> pdb=" O LEU S 36 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN S 194 " --> pdb=" O ALA S 118 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'S' and resid 99 through 101 removed outlier: 6.701A pdb=" N ARG S 123 " --> pdb=" O ALA S 100 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'T' and resid 10 through 13 Processing sheet with id= AL, first strand: chain 'T' and resid 33 through 37 removed outlier: 6.315A pdb=" N PHE T 65 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU T 36 " --> pdb=" O PHE T 65 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR T 67 " --> pdb=" O LEU T 36 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN T 194 " --> pdb=" O ALA T 118 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'T' and resid 99 through 101 removed outlier: 6.701A pdb=" N ARG T 123 " --> pdb=" O ALA T 100 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'U' and resid 10 through 13 Processing sheet with id= AO, first strand: chain 'U' and resid 33 through 37 removed outlier: 6.322A pdb=" N PHE U 65 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU U 36 " --> pdb=" O PHE U 65 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR U 67 " --> pdb=" O LEU U 36 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN U 194 " --> pdb=" O ALA U 118 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'U' and resid 99 through 101 removed outlier: 6.702A pdb=" N ARG U 123 " --> pdb=" O ALA U 100 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 10 through 13 Processing sheet with id= AR, first strand: chain 'H' and resid 33 through 37 removed outlier: 6.322A pdb=" N PHE H 65 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU H 36 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR H 67 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN H 194 " --> pdb=" O ALA H 118 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 99 through 101 removed outlier: 6.702A pdb=" N ARG H 123 " --> pdb=" O ALA H 100 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'I' and resid 10 through 15 removed outlier: 3.810A pdb=" N GLY I 18 " --> pdb=" O SER I 15 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'I' and resid 33 through 37 removed outlier: 6.316A pdb=" N PHE I 65 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU I 36 " --> pdb=" O PHE I 65 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR I 67 " --> pdb=" O LEU I 36 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN I 194 " --> pdb=" O ALA I 118 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'I' and resid 99 through 101 removed outlier: 6.701A pdb=" N ARG I 123 " --> pdb=" O ALA I 100 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'J' and resid 10 through 13 Processing sheet with id= AX, first strand: chain 'J' and resid 33 through 37 removed outlier: 6.316A pdb=" N PHE J 65 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU J 36 " --> pdb=" O PHE J 65 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR J 67 " --> pdb=" O LEU J 36 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN J 194 " --> pdb=" O ALA J 118 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'J' and resid 99 through 101 removed outlier: 6.702A pdb=" N ARG J 123 " --> pdb=" O ALA J 100 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'K' and resid 10 through 15 removed outlier: 3.609A pdb=" N GLY K 18 " --> pdb=" O SER K 15 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'K' and resid 33 through 37 removed outlier: 6.307A pdb=" N PHE K 65 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU K 36 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR K 67 " --> pdb=" O LEU K 36 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN K 194 " --> pdb=" O ALA K 118 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'K' and resid 99 through 101 removed outlier: 6.702A pdb=" N ARG K 123 " --> pdb=" O ALA K 100 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'M' and resid 33 through 37 removed outlier: 6.314A pdb=" N PHE M 65 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU M 36 " --> pdb=" O PHE M 65 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR M 67 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN M 194 " --> pdb=" O ALA M 118 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'M' and resid 99 through 101 removed outlier: 6.702A pdb=" N ARG M 123 " --> pdb=" O ALA M 100 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'N' and resid 10 through 13 Processing sheet with id= BF, first strand: chain 'N' and resid 33 through 37 removed outlier: 6.299A pdb=" N PHE N 65 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU N 36 " --> pdb=" O PHE N 65 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR N 67 " --> pdb=" O LEU N 36 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN N 194 " --> pdb=" O ALA N 118 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'N' and resid 99 through 101 removed outlier: 6.701A pdb=" N ARG N 123 " --> pdb=" O ALA N 100 " (cutoff:3.500A) 1604 hydrogen bonds defined for protein. 4383 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: 28.80 Time building geometry restraints manager: 51.67 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: 36850 1.03 - 1.23: 48 1.23 - 1.42: 14638 1.42 - 1.62: 22053 1.62 - 1.81: 262 Bond restraints: 73851 Sorted by residual: bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.04e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.98e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.91e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.88e+01 ... (remaining 73846 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.89: 1136 106.89 - 114.17: 92852 114.17 - 121.45: 26746 121.45 - 128.73: 13278 128.73 - 136.01: 105 Bond angle restraints: 134117 Sorted by residual: angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 121.88 17.99 1.00e+00 1.00e+00 3.24e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 122.07 17.80 1.00e+00 1.00e+00 3.17e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 122.10 17.77 1.00e+00 1.00e+00 3.16e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 122.16 17.71 1.00e+00 1.00e+00 3.14e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 122.35 17.52 1.00e+00 1.00e+00 3.07e+02 ... (remaining 134112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 31981 16.64 - 33.27: 1448 33.27 - 49.91: 585 49.91 - 66.54: 266 66.54 - 83.18: 30 Dihedral angle restraints: 34310 sinusoidal: 19358 harmonic: 14952 Sorted by residual: dihedral pdb=" CA ASN A 195 " pdb=" C ASN A 195 " pdb=" N PRO A 196 " pdb=" CA PRO A 196 " ideal model delta harmonic sigma weight residual 180.00 126.05 53.95 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA ILE A 198 " pdb=" C ILE A 198 " pdb=" N THR A 199 " pdb=" CA THR A 199 " ideal model delta harmonic sigma weight residual 180.00 147.20 32.80 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CA ASP A 194 " pdb=" C ASP A 194 " pdb=" N ASN A 195 " pdb=" CA ASN A 195 " ideal model delta harmonic sigma weight residual -180.00 -149.73 -30.27 0 5.00e+00 4.00e-02 3.67e+01 ... (remaining 34307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 4014 0.033 - 0.066: 1047 0.066 - 0.098: 437 0.098 - 0.131: 242 0.131 - 0.164: 7 Chirality restraints: 5747 Sorted by residual: chirality pdb=" C1' ATP A 501 " pdb=" C2' ATP A 501 " pdb=" N9 ATP A 501 " pdb=" O4' ATP A 501 " both_signs ideal model delta sigma weight residual False 2.41 2.57 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" C1' ATP C 501 " pdb=" C2' ATP C 501 " pdb=" N9 ATP C 501 " pdb=" O4' ATP C 501 " both_signs ideal model delta sigma weight residual False 2.41 2.57 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" C1' ATP B 501 " pdb=" C2' ATP B 501 " pdb=" N9 ATP B 501 " pdb=" O4' ATP B 501 " both_signs ideal model delta sigma weight residual False 2.41 2.56 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 5744 not shown) Planarity restraints: 10906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 195 " 0.060 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO A 196 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN K 59 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO K 60 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO K 60 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO K 60 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 138 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 139 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " -0.019 5.00e-02 4.00e+02 ... (remaining 10903 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 1721 2.10 - 2.72: 131850 2.72 - 3.35: 221012 3.35 - 3.97: 289817 3.97 - 4.60: 456554 Nonbonded interactions: 1100954 Sorted by model distance: nonbonded pdb=" H SER A 197 " pdb=" O UNK G 9 " model vdw 1.472 1.850 nonbonded pdb=" H PHE C 269 " pdb=" OH TYR I 67 " model vdw 1.567 1.850 nonbonded pdb=" O SER B 197 " pdb=" HZ2 LYS A 192 " model vdw 1.572 1.850 nonbonded pdb=" HZ3 LYS B 393 " pdb=" O PHE B 412 " model vdw 1.580 1.850 nonbonded pdb=" OD1 ASN C 75 " pdb=" HZ2 LYS C 85 " model vdw 1.596 1.850 ... (remaining 1100949 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 63 through 190 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 206 through 225 or \ resid 234 through 274 or (resid 283 and (name N or name CA or name C or name O o \ r name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 \ or name HG22 or name HG23)) or resid 284 through 412)) selection = (chain 'B' and (resid 63 through 190 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 206 through 274 or \ (resid 283 and (name N or name CA or name C or name O or name CB or name OG1 or \ name CG2 or name HA or name HB or name HG1 or name HG21 or name HG22 or name HG2 \ 3)) or resid 284 through 412)) selection = (chain 'C' and (resid 63 through 190 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 206 through 225 or \ resid 234 through 274 or (resid 283 and (name N or name CA or name C or name O o \ r name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 \ or name HG22 or name HG23)) or resid 284 through 412)) selection = (chain 'D' and (resid 63 through 190 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 206 through 225 or \ resid 234 through 274 or (resid 283 and (name N or name CA or name C or name O o \ r name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 \ or name HG22 or name HG23)) or resid 284 through 412)) selection = (chain 'E' and (resid 63 through 190 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 206 through 225 or \ (resid 234 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 or \ name HG3)) or resid 235 through 274 or (resid 283 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name HA or name HB or name H \ G1 or name HG21 or name HG22 or name HG23)) or resid 284 through 412)) selection = (chain 'F' and (resid 63 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 127 through 225 or resid 234 \ through 412)) } ncs_group { reference = (chain 'H' and (resid 6 through 12 or (resid 20 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 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 name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'I' and (resid 6 through 12 or (resid 20 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 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 name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'J' and (resid 6 through 12 or (resid 20 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 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 name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'K' and (resid 6 through 12 or (resid 20 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 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 name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'L' and (resid 6 through 12 or (resid 20 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 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 name HH21 or name HH22)) or \ resid 21 through 198)) selection = chain 'M' selection = (chain 'N' and (resid 6 through 12 or (resid 20 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 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 name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'O' and (resid 6 through 12 or (resid 20 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 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 name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'P' and (resid 6 through 12 or (resid 20 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 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 name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'Q' and (resid 6 through 12 or (resid 20 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 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 name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'R' and (resid 6 through 12 or (resid 20 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 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 name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'S' and (resid 6 through 12 or (resid 20 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 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 name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'T' and (resid 6 through 12 or (resid 20 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 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 name HH21 or name HH22)) or \ resid 21 through 198)) selection = (chain 'U' and (resid 6 through 12 or (resid 20 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 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 name HH21 or name HH22)) or \ resid 21 through 198)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.840 Extract box with map and model: 8.760 Check model and map are aligned: 0.850 Set scattering table: 0.550 Process input model: 189.280 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:9.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 215.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5781 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 : 0.003 0.084 36955 Z= 0.200 Angle : 0.598 17.989 49835 Z= 0.410 Chirality : 0.040 0.164 5747 Planarity : 0.003 0.091 6450 Dihedral : 10.939 83.175 14135 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.60 % Favored : 96.38 % Rotamer: Outliers : 0.10 % Allowed : 0.46 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.11), residues: 4588 helix: -0.73 (0.09), residues: 2327 sheet: -0.14 (0.20), residues: 610 loop : -1.17 (0.13), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 101 PHE 0.017 0.002 PHE N 65 TYR 0.007 0.001 TYR F 96 ARG 0.004 0.000 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 1395 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1391 time to evaluate : 4.498 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: B 160 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7874 (tp40) REVERT: F 216 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7178 (mt-10) REVERT: F 375 VAL cc_start: 0.7446 (t) cc_final: 0.7195 (p) REVERT: D 213 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8350 (tptm) REVERT: A 236 ILE cc_start: 0.7263 (mt) cc_final: 0.7060 (mt) REVERT: P 103 MET cc_start: 0.5007 (mmm) cc_final: 0.4621 (mpp) REVERT: M 144 ILE cc_start: 0.5934 (mt) cc_final: 0.5453 (mt) REVERT: N 127 HIS cc_start: 0.5950 (p90) cc_final: 0.5586 (p90) outliers start: 4 outliers final: 5 residues processed: 1393 average time/residue: 2.7309 time to fit residues: 4593.5769 Evaluate side-chains 726 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 721 time to evaluate : 4.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain K residue 165 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 391 optimal weight: 4.9990 chunk 351 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 237 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 363 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 221 optimal weight: 20.0000 chunk 270 optimal weight: 9.9990 chunk 421 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 GLN B 242 ASN E 73 ASN E 81 GLN D 185 GLN D 260 GLN A 279 ASN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 179 ASN U 46 ASN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 179 ASN H 46 ASN H 51 GLN H 138 GLN ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN K 46 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 36955 Z= 0.458 Angle : 0.649 11.011 49835 Z= 0.345 Chirality : 0.045 0.166 5747 Planarity : 0.005 0.091 6450 Dihedral : 8.097 81.009 5181 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.77 % Allowed : 17.16 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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: -0.61 (0.12), residues: 4588 helix: 0.22 (0.10), residues: 2358 sheet: -0.29 (0.19), residues: 628 loop : -1.25 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS P 127 PHE 0.022 0.002 PHE E 349 TYR 0.016 0.002 TYR F 96 ARG 0.010 0.001 ARG D 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 893 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 745 time to evaluate : 4.587 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: C 81 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7452 (mp-120) REVERT: C 269 PHE cc_start: 0.7892 (m-80) cc_final: 0.7642 (m-80) REVERT: C 407 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: E 141 VAL cc_start: 0.8799 (m) cc_final: 0.8587 (p) REVERT: E 255 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7207 (pm20) REVERT: E 381 ASP cc_start: 0.8138 (t0) cc_final: 0.7929 (t0) REVERT: F 159 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7142 (pp20) REVERT: F 175 LYS cc_start: 0.8070 (mmtt) cc_final: 0.7440 (mmtt) REVERT: F 406 ARG cc_start: 0.6765 (tpp80) cc_final: 0.6365 (ttp-110) REVERT: D 160 GLN cc_start: 0.8538 (tp40) cc_final: 0.8270 (mm-40) REVERT: D 260 GLN cc_start: 0.7698 (tt0) cc_final: 0.7103 (tm130) REVERT: D 342 MET cc_start: 0.8833 (mpp) cc_final: 0.8443 (tpp) REVERT: A 153 TYR cc_start: 0.8273 (m-80) cc_final: 0.8035 (m-80) REVERT: A 165 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7556 (tt) REVERT: A 236 ILE cc_start: 0.7275 (mt) cc_final: 0.7061 (mt) REVERT: A 342 MET cc_start: 0.8141 (mtp) cc_final: 0.7835 (mtp) REVERT: O 143 GLU cc_start: 0.5847 (OUTLIER) cc_final: 0.4855 (tm-30) REVERT: P 125 MET cc_start: 0.3811 (tmm) cc_final: 0.2938 (tmm) REVERT: P 141 ASP cc_start: 0.6331 (OUTLIER) cc_final: 0.6110 (t0) REVERT: Q 81 ILE cc_start: 0.5498 (OUTLIER) cc_final: 0.4987 (mp) REVERT: Q 181 MET cc_start: 0.5004 (mtm) cc_final: 0.4726 (mpp) REVERT: S 30 LYS cc_start: 0.5774 (OUTLIER) cc_final: 0.5163 (tppt) REVERT: U 99 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.5774 (pm20) REVERT: H 127 HIS cc_start: 0.5223 (OUTLIER) cc_final: 0.4598 (p-80) REVERT: M 7 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7110 (mp) REVERT: M 68 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7872 (tp) outliers start: 148 outliers final: 58 residues processed: 847 average time/residue: 2.6021 time to fit residues: 2686.9520 Evaluate side-chains 692 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 621 time to evaluate : 4.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 141 ASP Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 61 ASP Chi-restraints excluded: chain S residue 172 GLU Chi-restraints excluded: chain S residue 194 GLN Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 145 HIS Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain U residue 126 ILE Chi-restraints excluded: chain U residue 128 GLN Chi-restraints excluded: chain U residue 173 ARG Chi-restraints excluded: chain U residue 178 ASP Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 102 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 234 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 350 optimal weight: 8.9990 chunk 286 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 422 optimal weight: 10.0000 chunk 456 optimal weight: 7.9990 chunk 375 optimal weight: 3.9990 chunk 418 optimal weight: 7.9990 chunk 143 optimal weight: 0.5980 chunk 338 optimal weight: 9.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN E 101 HIS E 160 GLN E 360 GLN F 77 HIS L 46 ASN ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 ASN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN H 128 GLN H 138 GLN I 46 ASN I 121 ASN M 46 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 36955 Z= 0.502 Angle : 0.651 10.724 49835 Z= 0.345 Chirality : 0.046 0.163 5747 Planarity : 0.005 0.096 6450 Dihedral : 7.966 87.595 5173 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.89 % Allowed : 18.56 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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 (0.12), residues: 4588 helix: 0.26 (0.11), residues: 2372 sheet: -0.37 (0.20), residues: 636 loop : -1.29 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS N 145 PHE 0.021 0.002 PHE C 349 TYR 0.018 0.002 TYR E 153 ARG 0.009 0.001 ARG R 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 845 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 653 time to evaluate : 4.579 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: C 81 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7434 (mp-120) REVERT: C 269 PHE cc_start: 0.8064 (m-80) cc_final: 0.7847 (m-80) REVERT: E 255 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7529 (pm20) REVERT: E 256 LYS cc_start: 0.8357 (mtpt) cc_final: 0.8055 (mtmm) REVERT: F 159 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7116 (pp20) REVERT: F 182 TYR cc_start: 0.8581 (t80) cc_final: 0.8146 (t80) REVERT: F 375 VAL cc_start: 0.7587 (t) cc_final: 0.7354 (p) REVERT: F 406 ARG cc_start: 0.7070 (tpp80) cc_final: 0.6651 (ttp-110) REVERT: D 260 GLN cc_start: 0.7723 (tt0) cc_final: 0.7044 (tm130) REVERT: D 342 MET cc_start: 0.8989 (tpp) cc_final: 0.8710 (tpp) REVERT: D 403 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: A 153 TYR cc_start: 0.8395 (m-80) cc_final: 0.8175 (m-80) REVERT: A 156 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6873 (mt-10) REVERT: A 165 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7536 (tt) REVERT: A 213 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7641 (tppp) REVERT: A 293 ASP cc_start: 0.8396 (m-30) cc_final: 0.8185 (m-30) REVERT: A 342 MET cc_start: 0.8315 (mtp) cc_final: 0.8018 (mtp) REVERT: O 143 GLU cc_start: 0.5907 (OUTLIER) cc_final: 0.4902 (tm-30) REVERT: R 123 ARG cc_start: 0.5013 (OUTLIER) cc_final: 0.4781 (mpp80) REVERT: S 30 LYS cc_start: 0.5900 (OUTLIER) cc_final: 0.5290 (tppt) REVERT: H 127 HIS cc_start: 0.5162 (OUTLIER) cc_final: 0.4577 (p-80) REVERT: I 31 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7701 (mm-30) REVERT: M 7 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6923 (mp) REVERT: M 62 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8223 (mttp) REVERT: M 68 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8072 (tp) REVERT: N 20 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7729 (ttp-110) outliers start: 192 outliers final: 78 residues processed: 777 average time/residue: 2.6251 time to fit residues: 2483.3944 Evaluate side-chains 677 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 583 time to evaluate : 4.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 29 LEU Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 158 ARG Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 143 GLU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 61 ASP Chi-restraints excluded: chain S residue 194 GLN Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 145 HIS Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 181 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 155 LYS Chi-restraints excluded: chain M residue 182 SER Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 141 ASP Chi-restraints excluded: chain N residue 150 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 417 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 219 optimal weight: 30.0000 chunk 46 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 283 optimal weight: 20.0000 chunk 423 optimal weight: 9.9990 chunk 448 optimal weight: 7.9990 chunk 221 optimal weight: 8.9990 chunk 401 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN F 274 HIS D 160 GLN A 209 GLN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 GLN O 14 GLN ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 GLN U 46 ASN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN I 46 ASN I 51 GLN I 121 ASN K 14 GLN K 157 ASN M 138 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.100 36955 Z= 0.591 Angle : 0.686 10.584 49835 Z= 0.364 Chirality : 0.047 0.183 5747 Planarity : 0.006 0.097 6450 Dihedral : 8.178 83.184 5173 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.84 % Allowed : 19.56 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 4588 helix: 0.05 (0.10), residues: 2357 sheet: -0.57 (0.19), residues: 663 loop : -1.56 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS E 101 PHE 0.024 0.002 PHE C 349 TYR 0.020 0.002 TYR E 153 ARG 0.014 0.001 ARG S 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 810 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 620 time to evaluate : 4.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7540 (mp-120) REVERT: C 269 PHE cc_start: 0.8112 (m-80) cc_final: 0.7882 (m-80) REVERT: B 314 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: E 174 GLU cc_start: 0.7353 (tm-30) cc_final: 0.7096 (tm-30) REVERT: E 256 LYS cc_start: 0.8422 (mtpt) cc_final: 0.8167 (mtmm) REVERT: E 364 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7454 (mtt-85) REVERT: F 159 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7225 (pp20) REVERT: F 175 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7883 (mmtt) REVERT: F 182 TYR cc_start: 0.8588 (t80) cc_final: 0.8262 (t80) REVERT: F 344 ASN cc_start: 0.5484 (p0) cc_final: 0.4890 (t0) REVERT: F 375 VAL cc_start: 0.7676 (t) cc_final: 0.7422 (p) REVERT: F 382 THR cc_start: 0.7541 (OUTLIER) cc_final: 0.6959 (m) REVERT: F 406 ARG cc_start: 0.7264 (tpp80) cc_final: 0.6837 (ttp80) REVERT: F 410 LEU cc_start: 0.7568 (mt) cc_final: 0.7270 (mm) REVERT: D 260 GLN cc_start: 0.7750 (tt0) cc_final: 0.7151 (tm-30) REVERT: D 342 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8747 (tpp) REVERT: A 83 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7392 (mp-120) REVERT: A 156 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: A 165 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7554 (tt) REVERT: A 209 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7842 (tt0) REVERT: O 143 GLU cc_start: 0.5954 (OUTLIER) cc_final: 0.5028 (tm-30) REVERT: Q 81 ILE cc_start: 0.5435 (OUTLIER) cc_final: 0.5046 (mp) REVERT: R 123 ARG cc_start: 0.5197 (OUTLIER) cc_final: 0.4886 (mpp80) REVERT: S 30 LYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5227 (tppt) REVERT: U 99 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6206 (pm20) REVERT: H 127 HIS cc_start: 0.5552 (OUTLIER) cc_final: 0.4962 (p-80) REVERT: I 31 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7722 (mm-30) REVERT: I 154 GLU cc_start: 0.5145 (OUTLIER) cc_final: 0.4922 (tm-30) REVERT: K 64 ILE cc_start: 0.7827 (mt) cc_final: 0.7466 (mt) REVERT: M 7 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6915 (mp) REVERT: M 68 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8063 (tp) outliers start: 190 outliers final: 95 residues processed: 766 average time/residue: 2.6840 time to fit residues: 2503.8109 Evaluate side-chains 682 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 568 time to evaluate : 4.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 342 MET Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 178 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 158 ARG Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 143 GLU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 61 ASP Chi-restraints excluded: chain S residue 172 GLU Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 145 HIS Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain U residue 128 GLN Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 123 ARG Chi-restraints excluded: chain K residue 151 LYS Chi-restraints excluded: chain K residue 160 MET Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 155 LYS Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 141 ASP Chi-restraints excluded: chain N residue 150 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 373 optimal weight: 8.9990 chunk 254 optimal weight: 20.0000 chunk 6 optimal weight: 0.5980 chunk 333 optimal weight: 8.9990 chunk 185 optimal weight: 4.9990 chunk 382 optimal weight: 3.9990 chunk 310 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 229 optimal weight: 8.9990 chunk 402 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN B 260 GLN F 274 HIS L 46 ASN ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 GLN ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 ASN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 128 GLN I 46 ASN I 121 ASN I 179 ASN J 157 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 36955 Z= 0.339 Angle : 0.576 8.789 49835 Z= 0.300 Chirality : 0.043 0.148 5747 Planarity : 0.004 0.096 6450 Dihedral : 7.842 85.189 5173 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.82 % Allowed : 21.14 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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: -0.59 (0.12), residues: 4588 helix: 0.41 (0.11), residues: 2351 sheet: -0.51 (0.19), residues: 649 loop : -1.44 (0.14), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 101 PHE 0.015 0.001 PHE C 349 TYR 0.015 0.002 TYR E 153 ARG 0.013 0.001 ARG F 377 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 759 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 609 time to evaluate : 4.747 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: C 81 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7407 (mp-120) REVERT: C 154 VAL cc_start: 0.8987 (p) cc_final: 0.8650 (m) REVERT: B 160 GLN cc_start: 0.8610 (tp-100) cc_final: 0.8409 (tp40) REVERT: B 314 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: E 174 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7120 (tm-30) REVERT: E 256 LYS cc_start: 0.8317 (mtpt) cc_final: 0.8049 (mtmm) REVERT: F 159 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7225 (pp20) REVERT: F 175 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7861 (mmtt) REVERT: F 182 TYR cc_start: 0.8486 (t80) cc_final: 0.8247 (t80) REVERT: F 344 ASN cc_start: 0.5611 (p0) cc_final: 0.5026 (t0) REVERT: F 375 VAL cc_start: 0.7637 (t) cc_final: 0.7388 (p) REVERT: F 382 THR cc_start: 0.7160 (OUTLIER) cc_final: 0.6600 (m) REVERT: F 406 ARG cc_start: 0.7043 (tpp80) cc_final: 0.6656 (ttp-110) REVERT: F 410 LEU cc_start: 0.7390 (mt) cc_final: 0.7146 (mm) REVERT: D 260 GLN cc_start: 0.7723 (tt0) cc_final: 0.7106 (tm130) REVERT: D 403 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: A 81 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.6477 (mt0) REVERT: A 156 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: A 165 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7495 (tt) REVERT: O 143 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.5048 (tm-30) REVERT: P 157 ASN cc_start: 0.5446 (t0) cc_final: 0.5211 (t0) REVERT: Q 81 ILE cc_start: 0.5577 (OUTLIER) cc_final: 0.5223 (mp) REVERT: R 123 ARG cc_start: 0.5153 (OUTLIER) cc_final: 0.4847 (mpp80) REVERT: S 30 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5177 (tppt) REVERT: U 99 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.5838 (pm20) REVERT: H 62 LYS cc_start: 0.8331 (mttm) cc_final: 0.8120 (mmmm) REVERT: H 127 HIS cc_start: 0.5353 (OUTLIER) cc_final: 0.4730 (p-80) REVERT: I 31 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: J 168 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6719 (tp) REVERT: K 64 ILE cc_start: 0.7745 (mt) cc_final: 0.7425 (mt) REVERT: M 62 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8193 (mttp) REVERT: M 68 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8083 (tp) REVERT: M 152 ILE cc_start: 0.6957 (OUTLIER) cc_final: 0.6620 (mp) outliers start: 150 outliers final: 72 residues processed: 711 average time/residue: 2.7392 time to fit residues: 2397.4658 Evaluate side-chains 658 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 567 time to evaluate : 4.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 151 LYS Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 158 ARG Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 143 GLU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 172 GLU Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 123 ARG Chi-restraints excluded: chain K residue 151 LYS Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 155 LYS Chi-restraints excluded: chain M residue 182 SER Chi-restraints excluded: chain N residue 141 ASP Chi-restraints excluded: chain N residue 150 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 150 optimal weight: 0.5980 chunk 403 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 263 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 448 optimal weight: 10.0000 chunk 372 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 235 optimal weight: 20.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 GLN ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 ASN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN I 46 ASN I 51 GLN I 121 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 36955 Z= 0.350 Angle : 0.576 9.074 49835 Z= 0.299 Chirality : 0.043 0.145 5747 Planarity : 0.004 0.095 6450 Dihedral : 7.798 84.557 5173 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.82 % Allowed : 21.75 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.12), residues: 4588 helix: 0.55 (0.11), residues: 2350 sheet: -0.50 (0.19), residues: 669 loop : -1.43 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 101 PHE 0.016 0.002 PHE C 349 TYR 0.016 0.002 TYR F 96 ARG 0.013 0.001 ARG F 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 748 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 598 time to evaluate : 4.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7466 (mp-120) REVERT: C 98 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.7780 (mtm-85) REVERT: C 154 VAL cc_start: 0.8998 (p) cc_final: 0.8659 (m) REVERT: C 393 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7068 (mtmt) REVERT: B 160 GLN cc_start: 0.8578 (tp-100) cc_final: 0.8377 (tp40) REVERT: B 314 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: E 174 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7143 (tm-30) REVERT: E 256 LYS cc_start: 0.8350 (mtpt) cc_final: 0.8076 (mtmm) REVERT: E 364 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7448 (mtt-85) REVERT: E 376 GLU cc_start: 0.7699 (tp30) cc_final: 0.7492 (tp30) REVERT: F 159 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7208 (pp20) REVERT: F 175 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7901 (mmtt) REVERT: F 344 ASN cc_start: 0.5647 (p0) cc_final: 0.5052 (t0) REVERT: F 375 VAL cc_start: 0.7650 (t) cc_final: 0.7368 (p) REVERT: F 382 THR cc_start: 0.7347 (OUTLIER) cc_final: 0.6732 (p) REVERT: F 406 ARG cc_start: 0.7133 (tpp80) cc_final: 0.6779 (ttp80) REVERT: F 410 LEU cc_start: 0.7588 (mt) cc_final: 0.7361 (mm) REVERT: D 260 GLN cc_start: 0.7716 (tt0) cc_final: 0.7108 (tm130) REVERT: D 403 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: A 81 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.6502 (mt0) REVERT: A 83 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7381 (mp-120) REVERT: A 156 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: A 165 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7495 (tt) REVERT: O 143 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.5092 (tm-30) REVERT: P 177 ARG cc_start: 0.6127 (ttm-80) cc_final: 0.5865 (ttm170) REVERT: Q 81 ILE cc_start: 0.5451 (OUTLIER) cc_final: 0.5151 (mp) REVERT: R 48 VAL cc_start: 0.5391 (OUTLIER) cc_final: 0.4838 (t) REVERT: R 123 ARG cc_start: 0.5100 (OUTLIER) cc_final: 0.4777 (mpp80) REVERT: S 30 LYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5148 (tppt) REVERT: U 99 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.5989 (pm20) REVERT: H 62 LYS cc_start: 0.8335 (mttm) cc_final: 0.8125 (mmmm) REVERT: H 127 HIS cc_start: 0.5338 (OUTLIER) cc_final: 0.4657 (p-80) REVERT: I 31 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7671 (mm-30) REVERT: J 168 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6664 (tt) REVERT: K 64 ILE cc_start: 0.7761 (mt) cc_final: 0.7481 (mt) REVERT: M 62 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8206 (mttp) REVERT: M 152 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6620 (mp) outliers start: 150 outliers final: 78 residues processed: 709 average time/residue: 2.6674 time to fit residues: 2296.0692 Evaluate side-chains 674 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 573 time to evaluate : 4.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 369 ARG Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 151 LYS Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 158 ARG Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 143 GLU Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 172 GLU Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain U residue 125 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 123 ARG Chi-restraints excluded: chain K residue 151 LYS Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 155 LYS Chi-restraints excluded: chain M residue 182 SER Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain N residue 141 ASP Chi-restraints excluded: chain N residue 150 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 255 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 377 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 447 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN F 274 HIS L 46 ASN ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 198 ASN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 GLN ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 ASN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN I 121 ASN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.6387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.099 36955 Z= 0.588 Angle : 0.684 10.732 49835 Z= 0.360 Chirality : 0.047 0.157 5747 Planarity : 0.005 0.097 6450 Dihedral : 8.125 83.304 5173 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.66 % Allowed : 21.34 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.12), residues: 4588 helix: 0.12 (0.11), residues: 2348 sheet: -0.76 (0.19), residues: 643 loop : -1.71 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS E 101 PHE 0.023 0.002 PHE C 349 TYR 0.022 0.002 TYR F 96 ARG 0.014 0.001 ARG F 377 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 771 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 588 time to evaluate : 4.690 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: C 81 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7547 (mp-120) REVERT: C 98 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.7789 (mtm-85) REVERT: C 393 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7106 (mtmt) REVERT: B 314 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: E 174 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7244 (tm-30) REVERT: E 256 LYS cc_start: 0.8414 (mtpt) cc_final: 0.8106 (mtmm) REVERT: E 364 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7458 (mtt-85) REVERT: E 392 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7006 (tt) REVERT: F 159 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7216 (pp20) REVERT: F 175 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7945 (mmtt) REVERT: F 182 TYR cc_start: 0.8534 (t80) cc_final: 0.8222 (t80) REVERT: F 344 ASN cc_start: 0.5669 (p0) cc_final: 0.5117 (t0) REVERT: F 375 VAL cc_start: 0.7710 (t) cc_final: 0.7417 (p) REVERT: F 406 ARG cc_start: 0.7238 (tpp80) cc_final: 0.6832 (ttp-110) REVERT: D 260 GLN cc_start: 0.7673 (tt0) cc_final: 0.7081 (tm-30) REVERT: D 342 MET cc_start: 0.9012 (tpp) cc_final: 0.8695 (tpp) REVERT: D 403 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: A 81 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.6695 (mt0) REVERT: A 83 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7262 (mp-120) REVERT: A 156 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: A 160 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: A 165 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7534 (tt) REVERT: A 213 LYS cc_start: 0.8044 (tppp) cc_final: 0.7758 (tppp) REVERT: A 256 LYS cc_start: 0.8123 (mttt) cc_final: 0.7913 (mtpt) REVERT: A 264 LYS cc_start: 0.7005 (pmtt) cc_final: 0.6727 (pmtt) REVERT: O 143 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5197 (tm-30) REVERT: Q 81 ILE cc_start: 0.5431 (OUTLIER) cc_final: 0.5087 (mp) REVERT: R 48 VAL cc_start: 0.5678 (OUTLIER) cc_final: 0.5114 (t) REVERT: R 89 LYS cc_start: 0.5514 (mmpt) cc_final: 0.5070 (tttp) REVERT: R 123 ARG cc_start: 0.5152 (OUTLIER) cc_final: 0.4848 (mpp80) REVERT: S 30 LYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5240 (tppt) REVERT: U 99 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6226 (pm20) REVERT: H 62 LYS cc_start: 0.8356 (mttm) cc_final: 0.8144 (mmmm) REVERT: H 127 HIS cc_start: 0.5686 (OUTLIER) cc_final: 0.5100 (p-80) REVERT: I 31 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: M 7 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.7025 (mt) REVERT: M 152 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6889 (mp) outliers start: 183 outliers final: 106 residues processed: 720 average time/residue: 2.6417 time to fit residues: 2321.3279 Evaluate side-chains 673 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 544 time to evaluate : 4.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 369 ARG Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 151 LYS Chi-restraints excluded: chain O residue 152 ILE Chi-restraints excluded: chain O residue 168 LEU Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 158 ARG Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 81 ILE Chi-restraints excluded: chain Q residue 143 GLU Chi-restraints excluded: chain Q residue 193 ASP Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 172 GLU Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 84 THR Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain T residue 125 MET Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain U residue 19 GLU Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 85 MET Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 151 LYS Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 155 LYS Chi-restraints excluded: chain M residue 182 SER Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 141 ASP Chi-restraints excluded: chain N residue 150 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 276 optimal weight: 30.0000 chunk 178 optimal weight: 0.8980 chunk 267 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 284 optimal weight: 20.0000 chunk 304 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 351 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN E 160 GLN F 274 HIS ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 GLN T 46 ASN ** T 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN I 46 ASN I 121 ASN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36955 Z= 0.181 Angle : 0.541 7.747 49835 Z= 0.278 Chirality : 0.041 0.141 5747 Planarity : 0.004 0.095 6450 Dihedral : 7.613 88.326 5173 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.65 % Allowed : 23.50 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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: -0.28 (0.12), residues: 4588 helix: 0.80 (0.11), residues: 2333 sheet: -0.53 (0.20), residues: 634 loop : -1.42 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS T 127 PHE 0.019 0.001 PHE T 180 TYR 0.013 0.001 TYR F 96 ARG 0.015 0.000 ARG F 377 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 692 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 588 time to evaluate : 4.626 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: C 81 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7349 (mp-120) REVERT: C 154 VAL cc_start: 0.8964 (p) cc_final: 0.8706 (m) REVERT: C 393 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7133 (tttm) REVERT: E 256 LYS cc_start: 0.8314 (mtpt) cc_final: 0.8052 (mtmm) REVERT: E 364 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7465 (mtt-85) REVERT: F 175 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7938 (mmtt) REVERT: F 182 TYR cc_start: 0.8417 (t80) cc_final: 0.8080 (t80) REVERT: F 269 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.7053 (t80) REVERT: F 344 ASN cc_start: 0.5674 (p0) cc_final: 0.5185 (t0) REVERT: F 375 VAL cc_start: 0.7582 (t) cc_final: 0.7309 (p) REVERT: F 377 ARG cc_start: 0.7611 (mtm110) cc_final: 0.7187 (ttp80) REVERT: F 406 ARG cc_start: 0.7028 (tpp80) cc_final: 0.6608 (ttp-110) REVERT: D 260 GLN cc_start: 0.7669 (tt0) cc_final: 0.7096 (tm130) REVERT: D 274 HIS cc_start: 0.7560 (OUTLIER) cc_final: 0.7045 (p90) REVERT: D 342 MET cc_start: 0.8944 (tpp) cc_final: 0.8667 (tpp) REVERT: D 403 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: A 156 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: A 165 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7524 (tt) REVERT: A 209 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7827 (tt0) REVERT: A 264 LYS cc_start: 0.6818 (pmtt) cc_final: 0.6545 (pmtt) REVERT: L 189 TYR cc_start: 0.4037 (OUTLIER) cc_final: 0.3292 (t80) REVERT: O 89 LYS cc_start: 0.4647 (mmtm) cc_final: 0.4414 (mmtm) REVERT: P 177 ARG cc_start: 0.6023 (ttm-80) cc_final: 0.5815 (ttm170) REVERT: R 89 LYS cc_start: 0.5294 (mmpt) cc_final: 0.4949 (tttp) REVERT: R 123 ARG cc_start: 0.5118 (OUTLIER) cc_final: 0.4790 (mpp80) REVERT: U 99 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6019 (pm20) REVERT: H 127 HIS cc_start: 0.5316 (OUTLIER) cc_final: 0.4667 (p-80) REVERT: I 31 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7629 (mm-30) REVERT: K 64 ILE cc_start: 0.7733 (mt) cc_final: 0.7468 (mt) REVERT: K 181 MET cc_start: 0.6328 (OUTLIER) cc_final: 0.6114 (mtp) REVERT: M 62 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8195 (mttp) REVERT: M 152 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6712 (mp) outliers start: 104 outliers final: 53 residues processed: 656 average time/residue: 2.7611 time to fit residues: 2190.7704 Evaluate side-chains 632 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 563 time to evaluate : 4.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 269 PHE Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain L residue 189 TYR Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 151 LYS Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 158 ARG Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain S residue 172 GLU Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain T residue 125 MET Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 123 ARG Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 155 LYS Chi-restraints excluded: chain M residue 182 SER Chi-restraints excluded: chain M residue 194 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 406 optimal weight: 10.0000 chunk 428 optimal weight: 3.9990 chunk 390 optimal weight: 5.9990 chunk 416 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 chunk 181 optimal weight: 0.4980 chunk 327 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 376 optimal weight: 0.9980 chunk 394 optimal weight: 3.9990 chunk 415 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 160 GLN ** O 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 GLN T 46 ASN ** T 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 128 GLN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 138 GLN H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN H 198 ASN I 46 ASN I 121 ASN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 36955 Z= 0.264 Angle : 0.554 8.709 49835 Z= 0.285 Chirality : 0.042 0.145 5747 Planarity : 0.004 0.093 6450 Dihedral : 7.584 89.268 5173 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.22 % Allowed : 24.42 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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: -0.12 (0.12), residues: 4588 helix: 0.91 (0.11), residues: 2308 sheet: -0.47 (0.20), residues: 644 loop : -1.27 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS T 127 PHE 0.032 0.001 PHE P 35 TYR 0.016 0.001 TYR F 96 ARG 0.013 0.000 ARG F 377 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 666 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 579 time to evaluate : 4.679 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: C 81 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7436 (mp-120) REVERT: C 154 VAL cc_start: 0.8967 (p) cc_final: 0.8705 (m) REVERT: C 393 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6996 (mtmt) REVERT: E 256 LYS cc_start: 0.8343 (mtpt) cc_final: 0.8076 (mtmm) REVERT: E 364 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7474 (mtt-85) REVERT: F 175 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7956 (mmtt) REVERT: F 182 TYR cc_start: 0.8432 (t80) cc_final: 0.8185 (t80) REVERT: F 344 ASN cc_start: 0.5751 (p0) cc_final: 0.5277 (t0) REVERT: F 375 VAL cc_start: 0.7563 (t) cc_final: 0.7239 (p) REVERT: F 377 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7269 (ttp80) REVERT: F 406 ARG cc_start: 0.7000 (tpp80) cc_final: 0.6644 (ttp80) REVERT: D 160 GLN cc_start: 0.8662 (tp40) cc_final: 0.8423 (tp40) REVERT: D 260 GLN cc_start: 0.7686 (tt0) cc_final: 0.7088 (tm130) REVERT: D 274 HIS cc_start: 0.7665 (OUTLIER) cc_final: 0.6914 (p90) REVERT: D 342 MET cc_start: 0.8972 (tpp) cc_final: 0.8753 (tpp) REVERT: D 403 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: A 156 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: A 160 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: A 165 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7469 (tt) REVERT: A 209 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7832 (tt0) REVERT: A 264 LYS cc_start: 0.6875 (pmtt) cc_final: 0.6647 (pmtt) REVERT: L 189 TYR cc_start: 0.4082 (OUTLIER) cc_final: 0.3310 (t80) REVERT: R 89 LYS cc_start: 0.5225 (mmpt) cc_final: 0.4911 (tttp) REVERT: R 123 ARG cc_start: 0.5117 (OUTLIER) cc_final: 0.4787 (mpp80) REVERT: U 99 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6092 (pm20) REVERT: H 127 HIS cc_start: 0.5280 (OUTLIER) cc_final: 0.4616 (p-80) REVERT: I 31 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7653 (mm-30) REVERT: J 168 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6600 (tp) REVERT: K 181 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.6042 (mtp) REVERT: M 152 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6713 (mp) outliers start: 87 outliers final: 49 residues processed: 636 average time/residue: 2.7913 time to fit residues: 2166.0835 Evaluate side-chains 628 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 563 time to evaluate : 4.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain L residue 189 TYR Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 151 LYS Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 158 ARG Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain S residue 172 GLU Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain T residue 125 MET Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 123 ARG Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 155 LYS Chi-restraints excluded: chain M residue 182 SER Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain N residue 160 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 9.9990 chunk 440 optimal weight: 9.9990 chunk 268 optimal weight: 30.0000 chunk 209 optimal weight: 20.0000 chunk 306 optimal weight: 20.0000 chunk 462 optimal weight: 9.9990 chunk 425 optimal weight: 9.9990 chunk 368 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 284 optimal weight: 20.0000 chunk 225 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS B 260 GLN E 160 GLN F 101 HIS F 274 HIS ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 198 ASN ** O 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 GLN ** T 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 128 GLN U 46 ASN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN I 46 ASN I 51 GLN I 121 ASN ** N 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.121 36955 Z= 0.848 Angle : 0.800 12.039 49835 Z= 0.426 Chirality : 0.054 0.205 5747 Planarity : 0.006 0.095 6450 Dihedral : 8.331 84.127 5173 Min Nonbonded Distance : 1.536 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.37 % Allowed : 24.50 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.12), residues: 4588 helix: -0.15 (0.11), residues: 2303 sheet: -0.81 (0.20), residues: 643 loop : -1.82 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.002 HIS E 101 PHE 0.029 0.003 PHE C 349 TYR 0.026 0.003 TYR F 96 ARG 0.011 0.001 ARG A 377 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9176 Ramachandran restraints generated. 4588 Oldfield, 0 Emsley, 4588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Evaluate side-chains 650 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 557 time to evaluate : 4.533 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: C 81 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.7685 (mp-120) REVERT: C 98 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7831 (mtm-85) REVERT: C 393 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7152 (mtmt) REVERT: B 160 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8462 (tp40) REVERT: E 256 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8118 (mtmm) REVERT: E 364 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7451 (mtt-85) REVERT: F 175 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7919 (mmtt) REVERT: F 344 ASN cc_start: 0.5639 (p0) cc_final: 0.5141 (t0) REVERT: F 375 VAL cc_start: 0.7750 (t) cc_final: 0.7433 (p) REVERT: F 406 ARG cc_start: 0.7230 (tpp80) cc_final: 0.6770 (ttp-110) REVERT: D 260 GLN cc_start: 0.7707 (tt0) cc_final: 0.7083 (tm-30) REVERT: A 165 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7564 (tt) REVERT: A 256 LYS cc_start: 0.8179 (mttt) cc_final: 0.7960 (mtpp) REVERT: R 89 LYS cc_start: 0.5611 (mmpt) cc_final: 0.5234 (tttp) REVERT: R 123 ARG cc_start: 0.5101 (OUTLIER) cc_final: 0.4826 (mpp80) REVERT: U 99 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6395 (pm20) REVERT: H 127 HIS cc_start: 0.5743 (OUTLIER) cc_final: 0.5090 (p-80) outliers start: 93 outliers final: 58 residues processed: 626 average time/residue: 2.7688 time to fit residues: 2093.0507 Evaluate side-chains 601 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 535 time to evaluate : 4.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 151 LYS Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 96 CYS Chi-restraints excluded: chain P residue 158 ARG Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain R residue 123 ARG Chi-restraints excluded: chain S residue 172 GLU Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain T residue 125 MET Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 31 GLU Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 155 LYS Chi-restraints excluded: chain M residue 182 SER Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain N residue 103 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 292 optimal weight: 5.9990 chunk 392 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 339 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 368 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 378 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN B 260 GLN E 160 GLN F 274 HIS ** O 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 138 GLN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 GLN ** T 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 128 GLN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN I 121 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.195982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.142294 restraints weight = 136547.020| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.05 r_work: 0.3416 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.6602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36955 Z= 0.175 Angle : 0.553 6.784 49835 Z= 0.284 Chirality : 0.041 0.147 5747 Planarity : 0.004 0.094 6450 Dihedral : 7.582 88.900 5173 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.88 % Allowed : 25.21 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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: -0.35 (0.12), residues: 4588 helix: 0.73 (0.11), residues: 2310 sheet: -0.56 (0.20), residues: 620 loop : -1.40 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS T 127 PHE 0.023 0.001 PHE T 180 TYR 0.015 0.001 TYR F 182 ARG 0.014 0.001 ARG F 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33080.93 seconds wall clock time: 566 minutes 33.51 seconds (33993.51 seconds total)