Starting phenix.real_space_refine on Sun Feb 18 04:08:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl6_33273/02_2024/7xl6_33273.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl6_33273/02_2024/7xl6_33273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl6_33273/02_2024/7xl6_33273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl6_33273/02_2024/7xl6_33273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl6_33273/02_2024/7xl6_33273.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl6_33273/02_2024/7xl6_33273.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.075 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 13587 2.51 5 N 3430 2.21 5 O 3654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 57": "OE1" <-> "OE2" Residue "F ASP 139": "OD1" <-> "OD2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 325": "OD1" <-> "OD2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 325": "OD1" <-> "OD2" Residue "C TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 188": "OE1" <-> "OE2" Residue "E TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 325": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20783 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "A" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "B" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "C" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "D" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "E" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "G" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Time building chain proxies: 11.45, per 1000 atoms: 0.55 Number of scatterers: 20783 At special positions: 0 Unit cell: (124.5, 122.84, 125.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3654 8.00 N 3430 7.00 C 13587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.64 Conformation dependent library (CDL) restraints added in 3.4 seconds 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 14 sheets defined 61.6% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'F' and resid 2 through 11 removed outlier: 3.817A pdb=" N GLU F 9 " --> pdb=" O HIS F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 54 removed outlier: 4.137A pdb=" N SER F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 83 Processing helix chain 'F' and resid 104 through 121 removed outlier: 4.196A pdb=" N LYS F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Proline residue: F 111 - end of helix Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 132 through 148 Processing helix chain 'F' and resid 159 through 168 removed outlier: 3.598A pdb=" N LYS F 167 " --> pdb=" O LYS F 163 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER F 168 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 174 Processing helix chain 'F' and resid 177 through 183 removed outlier: 3.947A pdb=" N ALA F 181 " --> pdb=" O GLU F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 201 removed outlier: 3.865A pdb=" N ALA F 197 " --> pdb=" O GLU F 193 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 230 removed outlier: 3.564A pdb=" N LEU F 216 " --> pdb=" O ARG F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 296 removed outlier: 4.163A pdb=" N VAL F 277 " --> pdb=" O SER F 273 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR F 280 " --> pdb=" O SER F 276 " (cutoff:3.500A) Proline residue: F 285 - end of helix removed outlier: 3.748A pdb=" N ILE F 288 " --> pdb=" O VAL F 284 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU F 294 " --> pdb=" O ASN F 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 308 removed outlier: 3.754A pdb=" N MET F 307 " --> pdb=" O SER F 303 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU F 308 " --> pdb=" O VAL F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 317 removed outlier: 4.197A pdb=" N LEU F 313 " --> pdb=" O PRO F 309 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU F 314 " --> pdb=" O ALA F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 335 removed outlier: 3.587A pdb=" N VAL F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 366 removed outlier: 4.056A pdb=" N VAL F 365 " --> pdb=" O ASN F 361 " (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 375 Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.814A pdb=" N GLU A 9 " --> pdb=" O HIS A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 54 removed outlier: 4.124A pdb=" N SER A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 104 through 121 removed outlier: 4.200A pdb=" N LYS A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 132 through 148 Processing helix chain 'A' and resid 158 through 168 removed outlier: 3.921A pdb=" N LEU A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 177 through 183 removed outlier: 3.939A pdb=" N ALA A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 201 removed outlier: 3.781A pdb=" N ALA A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 230 removed outlier: 3.556A pdb=" N LEU A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.159A pdb=" N VAL A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) Proline residue: A 285 - end of helix removed outlier: 3.758A pdb=" N ILE A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.757A pdb=" N MET A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 317 removed outlier: 4.171A pdb=" N LEU A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.601A pdb=" N VAL A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 removed outlier: 4.058A pdb=" N VAL A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'B' and resid 3 through 11 removed outlier: 3.809A pdb=" N GLU B 9 " --> pdb=" O HIS B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 54 removed outlier: 4.129A pdb=" N SER B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 83 Processing helix chain 'B' and resid 104 through 121 removed outlier: 4.197A pdb=" N LYS B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 132 through 148 Processing helix chain 'B' and resid 158 through 168 removed outlier: 3.924A pdb=" N LEU B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 168 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.947A pdb=" N ALA B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.767A pdb=" N ALA B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 230 removed outlier: 3.567A pdb=" N LEU B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.096A pdb=" N VAL B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) Proline residue: B 285 - end of helix removed outlier: 3.745A pdb=" N ILE B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.752A pdb=" N MET B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 317 removed outlier: 4.176A pdb=" N LEU B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.594A pdb=" N VAL B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 366 removed outlier: 4.062A pdb=" N VAL B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'C' and resid 3 through 11 removed outlier: 3.810A pdb=" N GLU C 9 " --> pdb=" O HIS C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 54 removed outlier: 4.126A pdb=" N SER C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 83 Processing helix chain 'C' and resid 104 through 121 removed outlier: 4.189A pdb=" N LYS C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'C' and resid 159 through 168 removed outlier: 3.503A pdb=" N LYS C 163 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.931A pdb=" N ALA C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 removed outlier: 3.726A pdb=" N ALA C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 230 removed outlier: 3.563A pdb=" N LEU C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 296 removed outlier: 4.159A pdb=" N VAL C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) Proline residue: C 285 - end of helix removed outlier: 3.751A pdb=" N ILE C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.756A pdb=" N MET C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 308 " --> pdb=" O VAL C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 317 removed outlier: 4.176A pdb=" N LEU C 313 " --> pdb=" O PRO C 309 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.584A pdb=" N VAL C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 366 removed outlier: 4.063A pdb=" N VAL C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 369 No H-bonds generated for 'chain 'C' and resid 367 through 369' Processing helix chain 'C' and resid 371 through 375 Processing helix chain 'D' and resid 3 through 11 removed outlier: 3.812A pdb=" N GLU D 9 " --> pdb=" O HIS D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 54 removed outlier: 4.120A pdb=" N SER D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 83 Processing helix chain 'D' and resid 104 through 121 removed outlier: 4.187A pdb=" N LYS D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 132 through 148 Processing helix chain 'D' and resid 158 through 168 removed outlier: 3.928A pdb=" N LEU D 162 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 174 Processing helix chain 'D' and resid 177 through 183 removed outlier: 3.947A pdb=" N ALA D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.845A pdb=" N ALA D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 230 removed outlier: 3.562A pdb=" N LEU D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 296 removed outlier: 4.101A pdb=" N VAL D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR D 280 " --> pdb=" O SER D 276 " (cutoff:3.500A) Proline residue: D 285 - end of helix removed outlier: 3.752A pdb=" N ILE D 288 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.774A pdb=" N MET D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU D 308 " --> pdb=" O VAL D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 317 removed outlier: 4.189A pdb=" N LEU D 313 " --> pdb=" O PRO D 309 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.613A pdb=" N VAL D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 366 removed outlier: 4.060A pdb=" N VAL D 365 " --> pdb=" O ASN D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 369 No H-bonds generated for 'chain 'D' and resid 367 through 369' Processing helix chain 'D' and resid 371 through 375 Processing helix chain 'E' and resid 3 through 11 removed outlier: 3.815A pdb=" N GLU E 9 " --> pdb=" O HIS E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 54 removed outlier: 4.123A pdb=" N SER E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 83 Processing helix chain 'E' and resid 104 through 121 removed outlier: 4.212A pdb=" N LYS E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Proline residue: E 111 - end of helix Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 132 through 148 Processing helix chain 'E' and resid 158 through 168 removed outlier: 3.915A pdb=" N LEU E 162 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS E 167 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER E 168 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 174 Processing helix chain 'E' and resid 177 through 183 removed outlier: 3.937A pdb=" N ALA E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 201 removed outlier: 3.846A pdb=" N ALA E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 230 removed outlier: 3.553A pdb=" N LEU E 216 " --> pdb=" O ARG E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 296 removed outlier: 4.120A pdb=" N VAL E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR E 280 " --> pdb=" O SER E 276 " (cutoff:3.500A) Proline residue: E 285 - end of helix removed outlier: 3.747A pdb=" N ILE E 288 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.760A pdb=" N MET E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU E 308 " --> pdb=" O VAL E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 317 removed outlier: 4.175A pdb=" N LEU E 313 " --> pdb=" O PRO E 309 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 335 removed outlier: 3.603A pdb=" N VAL E 328 " --> pdb=" O ASN E 324 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 366 removed outlier: 4.065A pdb=" N VAL E 365 " --> pdb=" O ASN E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 369 No H-bonds generated for 'chain 'E' and resid 367 through 369' Processing helix chain 'E' and resid 371 through 375 Processing helix chain 'G' and resid 3 through 11 removed outlier: 3.821A pdb=" N GLU G 9 " --> pdb=" O HIS G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 54 removed outlier: 4.136A pdb=" N SER G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 83 Processing helix chain 'G' and resid 104 through 121 removed outlier: 4.205A pdb=" N LYS G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Proline residue: G 111 - end of helix Processing helix chain 'G' and resid 122 through 132 Processing helix chain 'G' and resid 132 through 148 Processing helix chain 'G' and resid 159 through 168 removed outlier: 3.602A pdb=" N LYS G 167 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER G 168 " --> pdb=" O ILE G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 174 Processing helix chain 'G' and resid 177 through 183 removed outlier: 3.945A pdb=" N ALA G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 201 removed outlier: 3.853A pdb=" N ALA G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 230 removed outlier: 3.558A pdb=" N LEU G 216 " --> pdb=" O ARG G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 282 removed outlier: 4.103A pdb=" N VAL G 277 " --> pdb=" O SER G 273 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR G 280 " --> pdb=" O SER G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 296 removed outlier: 3.749A pdb=" N ILE G 288 " --> pdb=" O VAL G 284 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS G 295 " --> pdb=" O LEU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 308 removed outlier: 3.751A pdb=" N MET G 307 " --> pdb=" O SER G 303 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU G 308 " --> pdb=" O VAL G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 317 removed outlier: 4.164A pdb=" N LEU G 313 " --> pdb=" O PRO G 309 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU G 314 " --> pdb=" O ALA G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 335 removed outlier: 3.603A pdb=" N VAL G 328 " --> pdb=" O ASN G 324 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA G 335 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 366 removed outlier: 4.058A pdb=" N VAL G 365 " --> pdb=" O ASN G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 369 No H-bonds generated for 'chain 'G' and resid 367 through 369' Processing helix chain 'G' and resid 371 through 375 Processing sheet with id=AA1, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'F' and resid 89 through 91 removed outlier: 3.592A pdb=" N LYS F 102 " --> pdb=" O HIS F 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.593A pdb=" N LYS A 102 " --> pdb=" O HIS A 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.588A pdb=" N LYS B 102 " --> pdb=" O HIS B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA8, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.591A pdb=" N LYS C 102 " --> pdb=" O HIS C 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AB1, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.586A pdb=" N LYS D 102 " --> pdb=" O HIS D 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AB3, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.592A pdb=" N LYS E 102 " --> pdb=" O HIS E 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 64 through 66 Processing sheet with id=AB5, first strand: chain 'G' and resid 89 through 91 removed outlier: 3.585A pdb=" N LYS G 102 " --> pdb=" O HIS G 90 " (cutoff:3.500A) 916 hydrogen bonds defined for protein. 2685 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: 5.68 Time building geometry restraints manager: 8.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6419 1.35 - 1.46: 5052 1.46 - 1.58: 9634 1.58 - 1.70: 0 1.70 - 1.81: 168 Bond restraints: 21273 Sorted by residual: bond pdb=" CA VAL C 284 " pdb=" CB VAL C 284 " ideal model delta sigma weight residual 1.537 1.543 -0.006 5.00e-03 4.00e+04 1.58e+00 bond pdb=" C VAL B 284 " pdb=" N PRO B 285 " ideal model delta sigma weight residual 1.337 1.352 -0.015 1.24e-02 6.50e+03 1.46e+00 bond pdb=" C VAL A 284 " pdb=" N PRO A 285 " ideal model delta sigma weight residual 1.337 1.351 -0.014 1.24e-02 6.50e+03 1.24e+00 bond pdb=" C VAL D 284 " pdb=" N PRO D 285 " ideal model delta sigma weight residual 1.337 1.351 -0.014 1.24e-02 6.50e+03 1.22e+00 bond pdb=" C VAL B 158 " pdb=" O VAL B 158 " ideal model delta sigma weight residual 1.241 1.229 0.012 1.06e-02 8.90e+03 1.20e+00 ... (remaining 21268 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.92: 611 106.92 - 113.70: 11967 113.70 - 120.49: 8524 120.49 - 127.27: 7515 127.27 - 134.05: 258 Bond angle restraints: 28875 Sorted by residual: angle pdb=" N VAL G 277 " pdb=" CA VAL G 277 " pdb=" C VAL G 277 " ideal model delta sigma weight residual 111.81 108.40 3.41 8.60e-01 1.35e+00 1.57e+01 angle pdb=" N VAL E 277 " pdb=" CA VAL E 277 " pdb=" C VAL E 277 " ideal model delta sigma weight residual 111.81 108.52 3.29 8.60e-01 1.35e+00 1.46e+01 angle pdb=" N VAL F 277 " pdb=" CA VAL F 277 " pdb=" C VAL F 277 " ideal model delta sigma weight residual 111.81 108.68 3.13 8.60e-01 1.35e+00 1.32e+01 angle pdb=" N VAL A 277 " pdb=" CA VAL A 277 " pdb=" C VAL A 277 " ideal model delta sigma weight residual 111.67 108.66 3.01 9.50e-01 1.11e+00 1.00e+01 angle pdb=" N VAL B 277 " pdb=" CA VAL B 277 " pdb=" C VAL B 277 " ideal model delta sigma weight residual 111.67 108.69 2.98 9.50e-01 1.11e+00 9.86e+00 ... (remaining 28870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.92: 9987 13.92 - 27.84: 1858 27.84 - 41.77: 679 41.77 - 55.69: 259 55.69 - 69.61: 55 Dihedral angle restraints: 12838 sinusoidal: 5138 harmonic: 7700 Sorted by residual: dihedral pdb=" CA ASN A 176 " pdb=" C ASN A 176 " pdb=" N GLU A 177 " pdb=" CA GLU A 177 " ideal model delta harmonic sigma weight residual 180.00 154.48 25.52 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ASN F 176 " pdb=" C ASN F 176 " pdb=" N GLU F 177 " pdb=" CA GLU F 177 " ideal model delta harmonic sigma weight residual 180.00 155.04 24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASN E 176 " pdb=" C ASN E 176 " pdb=" N GLU E 177 " pdb=" CA GLU E 177 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 12835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2112 0.030 - 0.059: 926 0.059 - 0.089: 226 0.089 - 0.118: 116 0.118 - 0.148: 8 Chirality restraints: 3388 Sorted by residual: chirality pdb=" CA ASP B 81 " pdb=" N ASP B 81 " pdb=" C ASP B 81 " pdb=" CB ASP B 81 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ASP C 81 " pdb=" N ASP C 81 " pdb=" C ASP C 81 " pdb=" CB ASP C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 3385 not shown) Planarity restraints: 3535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 105 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO C 106 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 106 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 106 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 105 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO A 106 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 106 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 106 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP F 105 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO F 106 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO F 106 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 106 " 0.021 5.00e-02 4.00e+02 ... (remaining 3532 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 293 2.67 - 3.23: 19065 3.23 - 3.78: 30318 3.78 - 4.34: 39752 4.34 - 4.90: 68051 Nonbonded interactions: 157479 Sorted by model distance: nonbonded pdb=" OD1 ASP F 139 " pdb=" OH TYR F 195 " model vdw 2.111 2.440 nonbonded pdb=" OD1 ASP A 139 " pdb=" OH TYR A 195 " model vdw 2.153 2.440 nonbonded pdb=" OD1 ASP G 139 " pdb=" OH TYR G 195 " model vdw 2.171 2.440 nonbonded pdb=" OD1 ASP D 139 " pdb=" OH TYR D 195 " model vdw 2.223 2.440 nonbonded pdb=" OD1 ASP C 139 " pdb=" OH TYR C 195 " model vdw 2.264 2.440 ... (remaining 157474 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.890 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: 0.010 Extract box with map and model: 8.060 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 52.540 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 0.002 0.041 21273 Z= 0.158 Angle : 0.581 10.113 28875 Z= 0.297 Chirality : 0.037 0.148 3388 Planarity : 0.003 0.038 3535 Dihedral : 17.806 69.609 7798 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.13 % Allowed : 31.37 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2534 helix: 0.67 (0.15), residues: 1428 sheet: None (None), residues: 0 loop : -2.80 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 175 HIS 0.003 0.000 HIS C 254 PHE 0.012 0.001 PHE C 269 TYR 0.007 0.001 TYR E 280 ARG 0.003 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 196 time to evaluate : 2.115 Fit side-chains REVERT: F 307 MET cc_start: 0.5767 (ttp) cc_final: 0.5512 (mtp) REVERT: A 193 GLU cc_start: 0.6793 (pm20) cc_final: 0.6518 (pm20) REVERT: C 316 ARG cc_start: 0.7261 (mtm-85) cc_final: 0.7027 (mtp-110) REVERT: E 318 MET cc_start: 0.6607 (tpp) cc_final: 0.6231 (tpp) REVERT: G 307 MET cc_start: 0.5724 (ttp) cc_final: 0.5477 (mtp) outliers start: 3 outliers final: 1 residues processed: 197 average time/residue: 0.2656 time to fit residues: 87.1036 Evaluate side-chains 168 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 305 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 197 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 ASN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21273 Z= 0.336 Angle : 0.664 9.055 28875 Z= 0.328 Chirality : 0.042 0.171 3388 Planarity : 0.005 0.048 3535 Dihedral : 4.605 44.409 2802 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.32 % Allowed : 29.97 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.68 (0.17), residues: 2534 helix: 0.12 (0.14), residues: 1533 sheet: None (None), residues: 0 loop : -3.18 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 297 HIS 0.006 0.001 HIS A 231 PHE 0.024 0.002 PHE D 269 TYR 0.023 0.002 TYR A 280 ARG 0.003 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 184 time to evaluate : 2.029 Fit side-chains revert: symmetry clash REVERT: F 318 MET cc_start: 0.7286 (tpp) cc_final: 0.6888 (tpp) REVERT: A 193 GLU cc_start: 0.7024 (pm20) cc_final: 0.6721 (pm20) REVERT: B 120 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8413 (mp) REVERT: E 120 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8463 (mp) outliers start: 102 outliers final: 63 residues processed: 269 average time/residue: 0.2449 time to fit residues: 111.9151 Evaluate side-chains 235 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 170 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 351 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 190 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 229 optimal weight: 0.7980 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21273 Z= 0.212 Angle : 0.567 8.829 28875 Z= 0.276 Chirality : 0.038 0.155 3388 Planarity : 0.004 0.045 3535 Dihedral : 4.299 45.179 2802 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.01 % Allowed : 32.01 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2534 helix: 0.46 (0.14), residues: 1512 sheet: None (None), residues: 0 loop : -3.14 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 297 HIS 0.003 0.001 HIS C 254 PHE 0.016 0.001 PHE G 269 TYR 0.015 0.001 TYR A 280 ARG 0.001 0.000 ARG F 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 171 time to evaluate : 2.199 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7063 (pm20) cc_final: 0.6766 (pm20) REVERT: B 339 GLU cc_start: 0.7456 (pm20) cc_final: 0.7216 (pm20) REVERT: C 139 ASP cc_start: 0.7548 (m-30) cc_final: 0.7302 (m-30) outliers start: 71 outliers final: 50 residues processed: 228 average time/residue: 0.2528 time to fit residues: 98.4076 Evaluate side-chains 218 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 168 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 71 ASN Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 343 PHE Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 365 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 109 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 243 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 218 optimal weight: 0.0770 chunk 65 optimal weight: 9.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21273 Z= 0.200 Angle : 0.553 8.093 28875 Z= 0.267 Chirality : 0.038 0.151 3388 Planarity : 0.004 0.045 3535 Dihedral : 4.156 46.324 2802 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.56 % Allowed : 31.88 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.18), residues: 2534 helix: 0.65 (0.15), residues: 1477 sheet: None (None), residues: 0 loop : -3.03 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 297 HIS 0.004 0.001 HIS C 254 PHE 0.018 0.001 PHE E 343 TYR 0.016 0.001 TYR A 280 ARG 0.001 0.000 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 179 time to evaluate : 2.478 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7070 (pm20) cc_final: 0.6784 (pm20) REVERT: B 120 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8481 (mp) REVERT: C 318 MET cc_start: 0.7286 (mmt) cc_final: 0.6484 (tpp) REVERT: E 349 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7800 (mm) REVERT: G 120 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8394 (mp) outliers start: 84 outliers final: 59 residues processed: 246 average time/residue: 0.2455 time to fit residues: 102.8837 Evaluate side-chains 229 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 167 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 343 PHE Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 365 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 100 optimal weight: 0.0570 chunk 207 optimal weight: 0.5980 chunk 168 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 218 optimal weight: 0.0050 chunk 61 optimal weight: 0.8980 overall best weight: 0.4312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 ASN ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21273 Z= 0.144 Angle : 0.526 7.616 28875 Z= 0.252 Chirality : 0.036 0.135 3388 Planarity : 0.003 0.043 3535 Dihedral : 3.909 46.930 2802 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.80 % Allowed : 33.28 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 2534 helix: 0.99 (0.15), residues: 1456 sheet: None (None), residues: 0 loop : -3.03 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 297 HIS 0.002 0.000 HIS F 254 PHE 0.014 0.001 PHE D 343 TYR 0.011 0.001 TYR A 280 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 179 time to evaluate : 2.358 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7007 (pm20) cc_final: 0.6760 (pm20) REVERT: B 120 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8453 (mp) REVERT: E 349 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7752 (mm) REVERT: G 120 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8395 (mp) outliers start: 66 outliers final: 48 residues processed: 230 average time/residue: 0.2511 time to fit residues: 98.8504 Evaluate side-chains 223 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 172 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 343 PHE Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 174 PHE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 71 ASN Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 343 PHE Chi-restraints excluded: chain G residue 365 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 10.0000 chunk 219 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 202 optimal weight: 0.0570 chunk 112 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 chunk 128 optimal weight: 6.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 ASN ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21273 Z= 0.156 Angle : 0.533 8.663 28875 Z= 0.253 Chirality : 0.037 0.140 3388 Planarity : 0.004 0.044 3535 Dihedral : 3.860 46.933 2802 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.43 % Allowed : 33.11 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.18), residues: 2534 helix: 1.02 (0.15), residues: 1463 sheet: None (None), residues: 0 loop : -2.99 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 297 HIS 0.003 0.000 HIS C 254 PHE 0.016 0.001 PHE F 343 TYR 0.012 0.001 TYR A 280 ARG 0.001 0.000 ARG F 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 176 time to evaluate : 2.390 Fit side-chains revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8330 (mp) REVERT: A 193 GLU cc_start: 0.7013 (pm20) cc_final: 0.6756 (pm20) REVERT: B 120 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8429 (mp) REVERT: E 349 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7799 (mm) REVERT: G 120 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8393 (mp) outliers start: 81 outliers final: 56 residues processed: 242 average time/residue: 0.2449 time to fit residues: 101.8222 Evaluate side-chains 235 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 175 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 71 ASN Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 343 PHE Chi-restraints excluded: chain G residue 365 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 ASN ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21273 Z= 0.165 Angle : 0.533 8.640 28875 Z= 0.254 Chirality : 0.037 0.142 3388 Planarity : 0.004 0.044 3535 Dihedral : 3.832 47.119 2802 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.39 % Allowed : 33.15 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2534 helix: 1.04 (0.15), residues: 1463 sheet: None (None), residues: 0 loop : -2.99 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 297 HIS 0.003 0.001 HIS C 254 PHE 0.016 0.001 PHE D 343 TYR 0.013 0.001 TYR A 280 ARG 0.001 0.000 ARG F 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 177 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8345 (mp) REVERT: A 193 GLU cc_start: 0.7012 (pm20) cc_final: 0.6757 (pm20) REVERT: B 120 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8431 (mp) REVERT: G 120 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8401 (mp) outliers start: 80 outliers final: 66 residues processed: 243 average time/residue: 0.2469 time to fit residues: 103.1724 Evaluate side-chains 245 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 176 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 174 PHE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 71 ASN Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 343 PHE Chi-restraints excluded: chain G residue 365 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.0030 chunk 96 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 73 optimal weight: 0.0070 chunk 47 optimal weight: 0.0870 chunk 154 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21273 Z= 0.140 Angle : 0.523 9.098 28875 Z= 0.248 Chirality : 0.036 0.145 3388 Planarity : 0.003 0.044 3535 Dihedral : 3.730 47.451 2802 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.97 % Allowed : 33.32 % Favored : 63.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.18), residues: 2534 helix: 1.16 (0.15), residues: 1463 sheet: None (None), residues: 0 loop : -2.98 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 297 HIS 0.002 0.000 HIS F 254 PHE 0.014 0.001 PHE D 343 TYR 0.011 0.001 TYR A 280 ARG 0.001 0.000 ARG E 334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 186 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8350 (mp) REVERT: A 193 GLU cc_start: 0.6986 (pm20) cc_final: 0.6740 (pm20) REVERT: B 120 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8441 (mp) REVERT: G 120 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8378 (mp) outliers start: 70 outliers final: 59 residues processed: 242 average time/residue: 0.2436 time to fit residues: 101.4163 Evaluate side-chains 242 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 180 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 174 PHE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 71 ASN Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 343 PHE Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 365 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 177 optimal weight: 0.0770 chunk 69 optimal weight: 0.7980 chunk 204 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN B 336 ASN ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 ASN E 336 ASN ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21273 Z= 0.163 Angle : 0.533 8.812 28875 Z= 0.253 Chirality : 0.037 0.146 3388 Planarity : 0.004 0.044 3535 Dihedral : 3.731 47.777 2802 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.05 % Allowed : 33.28 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.18), residues: 2534 helix: 1.02 (0.15), residues: 1505 sheet: None (None), residues: 0 loop : -3.03 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 297 HIS 0.003 0.000 HIS C 254 PHE 0.015 0.001 PHE G 269 TYR 0.012 0.001 TYR A 280 ARG 0.001 0.000 ARG C 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 180 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8361 (mp) REVERT: A 193 GLU cc_start: 0.6957 (pm20) cc_final: 0.6704 (pm20) REVERT: B 120 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8425 (mp) REVERT: G 120 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8412 (mp) outliers start: 72 outliers final: 57 residues processed: 239 average time/residue: 0.2447 time to fit residues: 100.9058 Evaluate side-chains 239 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 179 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 343 PHE Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 251 optimal weight: 30.0000 chunk 231 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN B 336 ASN ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 ASN E 336 ASN ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21273 Z= 0.213 Angle : 0.564 9.272 28875 Z= 0.271 Chirality : 0.038 0.165 3388 Planarity : 0.004 0.044 3535 Dihedral : 3.994 48.936 2802 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.88 % Allowed : 33.32 % Favored : 63.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.18), residues: 2534 helix: 0.90 (0.15), residues: 1491 sheet: None (None), residues: 0 loop : -2.97 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 297 HIS 0.004 0.001 HIS C 254 PHE 0.018 0.001 PHE G 269 TYR 0.016 0.001 TYR A 280 ARG 0.001 0.000 ARG F 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 172 time to evaluate : 2.092 Fit side-chains revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8485 (mp) REVERT: A 193 GLU cc_start: 0.7046 (pm20) cc_final: 0.6754 (pm20) REVERT: B 120 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8502 (mp) REVERT: D 140 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7400 (mp) REVERT: G 120 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8471 (mp) outliers start: 68 outliers final: 60 residues processed: 232 average time/residue: 0.2342 time to fit residues: 93.4150 Evaluate side-chains 233 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 169 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 184 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 205 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.211775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.163172 restraints weight = 24526.121| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.71 r_work: 0.3538 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21273 Z= 0.163 Angle : 0.547 9.188 28875 Z= 0.261 Chirality : 0.037 0.152 3388 Planarity : 0.004 0.044 3535 Dihedral : 3.934 49.587 2802 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.63 % Allowed : 33.62 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.18), residues: 2534 helix: 0.98 (0.15), residues: 1491 sheet: None (None), residues: 0 loop : -2.99 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 297 HIS 0.003 0.001 HIS C 254 PHE 0.014 0.001 PHE G 269 TYR 0.013 0.001 TYR A 280 ARG 0.002 0.000 ARG D 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3764.15 seconds wall clock time: 69 minutes 40.28 seconds (4180.28 seconds total)