Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 04:33:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/04_2023/6vfx_21194_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/04_2023/6vfx_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_21194/04_2023/6vfx_21194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/04_2023/6vfx_21194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/04_2023/6vfx_21194_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfx_21194/04_2023/6vfx_21194_trim_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-1.21rc1-4938/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: 23.34, 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: 52.08 Conformation dependent library (CDL) restraints added in 4.6 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: 3.00 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: 27.86 Time building geometry restraints manager: 54.54 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: 27683 16.64 - 33.27: 1071 33.27 - 49.91: 163 49.91 - 66.54: 79 66.54 - 83.18: 30 Dihedral angle restraints: 29026 sinusoidal: 14074 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 29023 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: 0.830 Extract box with map and model: 10.830 Check model and map are aligned: 0.810 Set scattering table: 0.520 Process input model: 184.490 Find NCS groups from input model: 3.290 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:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 214.330 ------------------------------------------------------------------------------- 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 : 10.545 83.175 13980 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 % 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 *********************** 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 : 4.549 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 outliers start: 4 outliers final: 5 residues processed: 1393 average time/residue: 2.7949 time to fit residues: 4722.7936 Evaluate side-chains 724 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 719 time to evaluate : 4.589 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 3 average time/residue: 0.7668 time to fit residues: 9.8759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 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: 7.9990 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 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 I 121 ASN K 46 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.4158 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= 0.461 Angle : 0.653 10.962 49835 Z= 0.347 Chirality : 0.045 0.160 5747 Planarity : 0.005 0.092 6450 Dihedral : 5.799 86.898 5016 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 3.79 % 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: 0.23 (0.10), residues: 2358 sheet: -0.23 (0.19), residues: 642 loop : -1.27 (0.14), residues: 1588 *********************** 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: 149 poor density : 744 time to evaluate : 4.659 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 outliers start: 149 outliers final: 62 residues processed: 845 average time/residue: 2.6489 time to fit residues: 2735.6554 Evaluate side-chains 696 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 634 time to evaluate : 4.647 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 62 outliers final: 48 residues processed: 17 average time/residue: 1.5481 time to fit residues: 42.4859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 350 optimal weight: 9.9990 chunk 286 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 422 optimal weight: 9.9990 chunk 456 optimal weight: 10.0000 chunk 375 optimal weight: 2.9990 chunk 418 optimal weight: 7.9990 chunk 143 optimal weight: 0.6980 chunk 338 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN E 81 GLN E 101 HIS E 160 GLN E 360 GLN F 77 HIS ** 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** 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: 0.6163 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.078 36955 Z= 0.479 Angle : 0.640 10.741 49835 Z= 0.338 Chirality : 0.045 0.158 5747 Planarity : 0.005 0.097 6450 Dihedral : 5.856 82.280 5016 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 4.74 % 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: -0.53 (0.12), residues: 4588 helix: 0.35 (0.11), residues: 2367 sheet: -0.38 (0.20), residues: 641 loop : -1.28 (0.14), residues: 1580 *********************** 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 856 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 670 time to evaluate : 4.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 186 outliers final: 83 residues processed: 792 average time/residue: 2.6450 time to fit residues: 2558.6582 Evaluate side-chains 672 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 589 time to evaluate : 4.637 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 69 residues processed: 15 average time/residue: 1.2657 time to fit residues: 33.3152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 219 optimal weight: 30.0000 chunk 46 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 283 optimal weight: 6.9990 chunk 423 optimal weight: 2.9990 chunk 448 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 401 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN A 209 GLN L 46 ASN L 138 GLN O 14 GLN ** 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** S 194 GLN U 46 ASN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 179 ASN H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN H 138 GLN I 46 ASN I 51 GLN I 121 ASN K 157 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.081 36955 Z= 0.511 Angle : 0.653 10.315 49835 Z= 0.343 Chirality : 0.046 0.149 5747 Planarity : 0.005 0.098 6450 Dihedral : 5.919 79.927 5016 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 4.48 % 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: -0.74 (0.12), residues: 4588 helix: 0.24 (0.11), residues: 2362 sheet: -0.56 (0.19), residues: 662 loop : -1.44 (0.14), residues: 1564 *********************** 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 802 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 626 time to evaluate : 4.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 176 outliers final: 91 residues processed: 758 average time/residue: 2.6968 time to fit residues: 2495.3164 Evaluate side-chains 665 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 574 time to evaluate : 4.589 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 75 residues processed: 17 average time/residue: 1.1494 time to fit residues: 35.1319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 373 optimal weight: 2.9990 chunk 254 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 333 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 382 optimal weight: 20.0000 chunk 310 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 229 optimal weight: 8.9990 chunk 402 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN L 46 ASN ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 86 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** U 138 GLN H 46 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 128 GLN ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN I 121 ASN J 157 ASN ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 36955 Z= 0.294 Angle : 0.562 8.660 49835 Z= 0.290 Chirality : 0.042 0.159 5747 Planarity : 0.004 0.096 6450 Dihedral : 5.549 75.311 5016 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 3.51 % 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: -0.37 (0.12), residues: 4588 helix: 0.59 (0.11), residues: 2367 sheet: -0.40 (0.20), residues: 650 loop : -1.35 (0.14), residues: 1571 *********************** 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 744 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 606 time to evaluate : 5.286 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 outliers start: 138 outliers final: 82 residues processed: 716 average time/residue: 2.7305 time to fit residues: 2379.9427 Evaluate side-chains 656 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 574 time to evaluate : 4.590 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 75 residues processed: 8 average time/residue: 1.0091 time to fit residues: 18.4550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 150 optimal weight: 0.9980 chunk 403 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 263 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 448 optimal weight: 8.9990 chunk 372 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 37 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 235 optimal weight: 20.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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** ** 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 I 179 ASN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 36955 Z= 0.316 Angle : 0.565 9.167 49835 Z= 0.292 Chirality : 0.042 0.151 5747 Planarity : 0.004 0.095 6450 Dihedral : 5.495 76.810 5016 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 3.87 % 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: -0.29 (0.12), residues: 4588 helix: 0.73 (0.11), residues: 2351 sheet: -0.41 (0.19), residues: 650 loop : -1.42 (0.14), residues: 1587 *********************** 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 746 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 594 time to evaluate : 4.705 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 outliers start: 152 outliers final: 88 residues processed: 709 average time/residue: 2.6844 time to fit residues: 2341.3064 Evaluate side-chains 655 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 567 time to evaluate : 4.656 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 76 residues processed: 13 average time/residue: 1.2183 time to fit residues: 29.5235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 327 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 377 optimal weight: 9.9990 chunk 250 optimal weight: 7.9990 chunk 447 optimal weight: 0.9990 chunk 279 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 chunk 206 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN L 46 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 GLN ** 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 121 ASN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 36955 Z= 0.351 Angle : 0.577 8.693 49835 Z= 0.298 Chirality : 0.042 0.152 5747 Planarity : 0.004 0.095 6450 Dihedral : 5.502 78.043 5016 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 3.26 % 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: -0.33 (0.12), residues: 4588 helix: 0.71 (0.11), residues: 2354 sheet: -0.43 (0.20), residues: 650 loop : -1.46 (0.14), residues: 1584 *********************** 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 719 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 591 time to evaluate : 4.680 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 outliers start: 128 outliers final: 81 residues processed: 692 average time/residue: 2.6966 time to fit residues: 2291.7238 Evaluate side-chains 641 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 560 time to evaluate : 4.666 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 77 residues processed: 6 average time/residue: 0.9983 time to fit residues: 15.5343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 276 optimal weight: 20.0000 chunk 178 optimal weight: 0.8980 chunk 267 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 284 optimal weight: 20.0000 chunk 304 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 351 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 L 46 ASN ** 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** 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 51 GLN I 121 ASN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 36955 Z= 0.201 Angle : 0.529 7.080 49835 Z= 0.269 Chirality : 0.041 0.146 5747 Planarity : 0.004 0.094 6450 Dihedral : 5.192 73.366 5016 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 3.00 % 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: 0.07 (0.12), residues: 4588 helix: 1.08 (0.11), residues: 2340 sheet: -0.35 (0.20), residues: 637 loop : -1.27 (0.15), residues: 1611 *********************** 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 709 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 591 time to evaluate : 4.666 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 outliers start: 118 outliers final: 78 residues processed: 683 average time/residue: 2.6159 time to fit residues: 2198.7048 Evaluate side-chains 634 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 556 time to evaluate : 5.010 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 71 residues processed: 7 average time/residue: 1.1468 time to fit residues: 18.0797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 390 optimal weight: 6.9990 chunk 416 optimal weight: 0.0070 chunk 250 optimal weight: 9.9990 chunk 181 optimal weight: 0.7980 chunk 327 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 376 optimal weight: 3.9990 chunk 394 optimal weight: 5.9990 chunk 415 optimal weight: 3.9990 overall best weight: 2.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 46 ASN ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** 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** ** 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 I 46 ASN I 121 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 36955 Z= 0.330 Angle : 0.568 9.298 49835 Z= 0.291 Chirality : 0.042 0.148 5747 Planarity : 0.004 0.094 6450 Dihedral : 5.345 75.288 5016 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 2.60 % 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: -0.08 (0.12), residues: 4588 helix: 0.94 (0.11), residues: 2353 sheet: -0.37 (0.20), residues: 650 loop : -1.37 (0.15), residues: 1585 *********************** 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 667 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 565 time to evaluate : 4.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 74 residues processed: 647 average time/residue: 2.6707 time to fit residues: 2114.5461 Evaluate side-chains 628 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 554 time to evaluate : 4.640 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 69 residues processed: 5 average time/residue: 0.7862 time to fit residues: 12.7360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 10.0000 chunk 440 optimal weight: 9.9990 chunk 268 optimal weight: 30.0000 chunk 209 optimal weight: 20.0000 chunk 306 optimal weight: 0.9980 chunk 462 optimal weight: 9.9990 chunk 425 optimal weight: 8.9990 chunk 368 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 284 optimal weight: 20.0000 chunk 225 optimal weight: 9.9990 overall best weight: 5.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 77 HIS B 260 GLN F 209 GLN F 274 HIS L 46 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN I 121 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.6561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.093 36955 Z= 0.607 Angle : 0.701 12.160 49835 Z= 0.368 Chirality : 0.048 0.160 5747 Planarity : 0.005 0.095 6450 Dihedral : 5.965 80.179 5016 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.09 % 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: -0.84 (0.12), residues: 4588 helix: 0.27 (0.11), residues: 2325 sheet: -0.55 (0.19), residues: 719 loop : -1.72 (0.14), residues: 1544 ********************** 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 657 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 557 time to evaluate : 4.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 76 residues processed: 639 average time/residue: 2.6956 time to fit residues: 2112.9511 Evaluate side-chains 608 residues out of total 3927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 532 time to evaluate : 4.805 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 68 residues processed: 8 average time/residue: 0.8225 time to fit residues: 18.8364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 292 optimal weight: 9.9990 chunk 392 optimal weight: 7.9990 chunk 112 optimal weight: 0.5980 chunk 339 optimal weight: 9.9990 chunk 54 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 368 optimal weight: 9.9990 chunk 154 optimal weight: 0.5980 chunk 378 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Q 99 GLN ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 GLN ** 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** I 46 ASN I 121 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.196168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.141555 restraints weight = 137211.137| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.08 r_work: 0.3442 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.6470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 36955 Z= 0.169 Angle : 0.539 6.870 49835 Z= 0.274 Chirality : 0.041 0.154 5747 Planarity : 0.004 0.095 6450 Dihedral : 5.230 68.293 5016 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 2.04 % 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: -0.08 (0.12), residues: 4588 helix: 0.99 (0.11), residues: 2333 sheet: -0.44 (0.20), residues: 617 loop : -1.39 (0.14), residues: 1638 =============================================================================== Job complete usr+sys time: 32814.51 seconds wall clock time: 562 minutes 20.76 seconds (33740.76 seconds total)