Starting phenix.real_space_refine on Mon Apr 6 01:40:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m68_30116/04_2026/6m68_30116.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m68_30116/04_2026/6m68_30116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m68_30116/04_2026/6m68_30116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m68_30116/04_2026/6m68_30116.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m68_30116/04_2026/6m68_30116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m68_30116/04_2026/6m68_30116.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.028 sd= 0.157 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 70 5.16 5 C 9975 2.51 5 N 2303 2.21 5 O 2590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14938 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 1.80, per 1000 atoms: 0.12 Number of scatterers: 14938 At special positions: 0 Unit cell: (113.4, 113.4, 116.64, 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 70 16.00 O 2590 8.00 N 2303 7.00 C 9975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.06 Conformation dependent library (CDL) restraints added in 623.5 milliseconds 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 69.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 35 through 59 removed outlier: 4.483A pdb=" N ILE A 41 " --> pdb=" O MET A 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 44 " --> pdb=" O CYS A 40 " (cutoff:3.500A) Proline residue: A 46 - end of helix removed outlier: 3.601A pdb=" N LEU A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.595A pdb=" N ALA A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.407A pdb=" N HIS A 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 107 " --> pdb=" O TRP A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' Processing helix chain 'A' and resid 108 through 129 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 156 removed outlier: 3.644A pdb=" N ASP A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 207 through 238 removed outlier: 4.234A pdb=" N ILE A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 254 Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 276 through 286 removed outlier: 4.176A pdb=" N ASN A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.752A pdb=" N VAL A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 317 through 320 Processing helix chain 'A' and resid 328 through 336 removed outlier: 4.188A pdb=" N ASN A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 59 removed outlier: 4.484A pdb=" N ILE B 41 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 44 " --> pdb=" O CYS B 40 " (cutoff:3.500A) Proline residue: B 46 - end of helix removed outlier: 3.601A pdb=" N LEU B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 50 " --> pdb=" O PRO B 46 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.595A pdb=" N ALA B 78 " --> pdb=" O TRP B 74 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 4.408A pdb=" N HIS B 106 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 107 " --> pdb=" O TRP B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 107' Processing helix chain 'B' and resid 108 through 129 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 156 removed outlier: 3.645A pdb=" N ASP B 147 " --> pdb=" O MET B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 207 through 238 removed outlier: 4.234A pdb=" N ILE B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG B 217 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 276 through 286 removed outlier: 4.175A pdb=" N ASN B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 removed outlier: 3.753A pdb=" N VAL B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 316 Processing helix chain 'B' and resid 317 through 320 Processing helix chain 'B' and resid 328 through 336 removed outlier: 4.187A pdb=" N ASN B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 59 removed outlier: 4.483A pdb=" N ILE C 41 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 44 " --> pdb=" O CYS C 40 " (cutoff:3.500A) Proline residue: C 46 - end of helix removed outlier: 3.601A pdb=" N LEU C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 50 " --> pdb=" O PRO C 46 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.596A pdb=" N ALA C 78 " --> pdb=" O TRP C 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.408A pdb=" N HIS C 106 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 107 " --> pdb=" O TRP C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 107' Processing helix chain 'C' and resid 108 through 129 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 156 removed outlier: 3.644A pdb=" N ASP C 147 " --> pdb=" O MET C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 207 through 238 removed outlier: 4.234A pdb=" N ILE C 211 " --> pdb=" O ASN C 207 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG C 217 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR C 234 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 254 Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 276 through 286 removed outlier: 4.176A pdb=" N ASN C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 removed outlier: 3.753A pdb=" N VAL C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 316 Processing helix chain 'C' and resid 317 through 320 Processing helix chain 'C' and resid 328 through 336 removed outlier: 4.187A pdb=" N ASN C 332 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 59 removed outlier: 4.483A pdb=" N ILE D 41 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY D 44 " --> pdb=" O CYS D 40 " (cutoff:3.500A) Proline residue: D 46 - end of helix removed outlier: 3.601A pdb=" N LEU D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 50 " --> pdb=" O PRO D 46 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 58 " --> pdb=" O PHE D 54 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 removed outlier: 3.596A pdb=" N ALA D 78 " --> pdb=" O TRP D 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS D 84 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 removed outlier: 4.407A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS D 107 " --> pdb=" O TRP D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 107' Processing helix chain 'D' and resid 108 through 129 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 156 removed outlier: 3.645A pdb=" N ASP D 147 " --> pdb=" O MET D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 198 through 203 Processing helix chain 'D' and resid 207 through 238 removed outlier: 4.234A pdb=" N ILE D 211 " --> pdb=" O ASN D 207 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 218 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR D 234 " --> pdb=" O TYR D 230 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 254 Processing helix chain 'D' and resid 269 through 274 Processing helix chain 'D' and resid 276 through 286 removed outlier: 4.176A pdb=" N ASN D 280 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 removed outlier: 3.752A pdb=" N VAL D 291 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 316 Processing helix chain 'D' and resid 317 through 320 Processing helix chain 'D' and resid 328 through 336 removed outlier: 4.187A pdb=" N ASN D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 59 removed outlier: 4.483A pdb=" N ILE E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY E 44 " --> pdb=" O CYS E 40 " (cutoff:3.500A) Proline residue: E 46 - end of helix removed outlier: 3.601A pdb=" N LEU E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 50 " --> pdb=" O PRO E 46 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE E 58 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 87 removed outlier: 3.596A pdb=" N ALA E 78 " --> pdb=" O TRP E 74 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS E 84 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 removed outlier: 4.408A pdb=" N HIS E 106 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS E 107 " --> pdb=" O TRP E 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 107' Processing helix chain 'E' and resid 108 through 129 Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 156 removed outlier: 3.645A pdb=" N ASP E 147 " --> pdb=" O MET E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 198 through 203 Processing helix chain 'E' and resid 207 through 238 removed outlier: 4.235A pdb=" N ILE E 211 " --> pdb=" O ASN E 207 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG E 217 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE E 222 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR E 234 " --> pdb=" O TYR E 230 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 254 Processing helix chain 'E' and resid 269 through 274 Processing helix chain 'E' and resid 276 through 286 removed outlier: 4.176A pdb=" N ASN E 280 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 removed outlier: 3.753A pdb=" N VAL E 291 " --> pdb=" O LEU E 287 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 316 Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 328 through 336 removed outlier: 4.187A pdb=" N ASN E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 59 removed outlier: 4.483A pdb=" N ILE F 41 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY F 44 " --> pdb=" O CYS F 40 " (cutoff:3.500A) Proline residue: F 46 - end of helix removed outlier: 3.601A pdb=" N LEU F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 50 " --> pdb=" O PRO F 46 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE F 58 " --> pdb=" O PHE F 54 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 removed outlier: 3.596A pdb=" N ALA F 78 " --> pdb=" O TRP F 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS F 84 " --> pdb=" O VAL F 80 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 107 removed outlier: 4.407A pdb=" N HIS F 106 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS F 107 " --> pdb=" O TRP F 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 103 through 107' Processing helix chain 'F' and resid 108 through 129 Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 156 removed outlier: 3.644A pdb=" N ASP F 147 " --> pdb=" O MET F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 198 through 203 Processing helix chain 'F' and resid 207 through 238 removed outlier: 4.235A pdb=" N ILE F 211 " --> pdb=" O ASN F 207 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG F 217 " --> pdb=" O TYR F 213 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU F 218 " --> pdb=" O ILE F 214 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE F 222 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR F 234 " --> pdb=" O TYR F 230 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 254 Processing helix chain 'F' and resid 269 through 274 Processing helix chain 'F' and resid 276 through 286 removed outlier: 4.176A pdb=" N ASN F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU F 281 " --> pdb=" O SER F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 295 removed outlier: 3.752A pdb=" N VAL F 291 " --> pdb=" O LEU F 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 316 Processing helix chain 'F' and resid 317 through 320 Processing helix chain 'F' and resid 328 through 336 removed outlier: 4.187A pdb=" N ASN F 332 " --> pdb=" O LEU F 328 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 59 removed outlier: 4.483A pdb=" N ILE G 41 " --> pdb=" O MET G 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY G 44 " --> pdb=" O CYS G 40 " (cutoff:3.500A) Proline residue: G 46 - end of helix removed outlier: 3.601A pdb=" N LEU G 49 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE G 50 " --> pdb=" O PRO G 46 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE G 58 " --> pdb=" O PHE G 54 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 removed outlier: 3.595A pdb=" N ALA G 78 " --> pdb=" O TRP G 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS G 84 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA G 86 " --> pdb=" O SER G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 107 removed outlier: 4.407A pdb=" N HIS G 106 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS G 107 " --> pdb=" O TRP G 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 103 through 107' Processing helix chain 'G' and resid 108 through 129 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 156 removed outlier: 3.645A pdb=" N ASP G 147 " --> pdb=" O MET G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 207 through 238 removed outlier: 4.235A pdb=" N ILE G 211 " --> pdb=" O ASN G 207 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG G 217 " --> pdb=" O TYR G 213 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU G 218 " --> pdb=" O ILE G 214 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE G 222 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR G 234 " --> pdb=" O TYR G 230 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE G 235 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER G 236 " --> pdb=" O GLY G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 254 Processing helix chain 'G' and resid 269 through 274 Processing helix chain 'G' and resid 276 through 286 removed outlier: 4.175A pdb=" N ASN G 280 " --> pdb=" O LEU G 276 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU G 281 " --> pdb=" O SER G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 295 removed outlier: 3.752A pdb=" N VAL G 291 " --> pdb=" O LEU G 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 316 Processing helix chain 'G' and resid 317 through 320 Processing helix chain 'G' and resid 328 through 336 removed outlier: 4.188A pdb=" N ASN G 332 " --> pdb=" O LEU G 328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU G 336 " --> pdb=" O ASN G 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 3.583A pdb=" N SER A 65 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.584A pdb=" N SER B 65 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.584A pdb=" N SER C 65 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 removed outlier: 3.584A pdb=" N SER D 65 " --> pdb=" O LYS D 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.583A pdb=" N SER E 65 " --> pdb=" O LYS E 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 removed outlier: 3.584A pdb=" N SER F 65 " --> pdb=" O LYS F 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 removed outlier: 3.584A pdb=" N SER G 65 " --> pdb=" O LYS G 266 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1893 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: 1.90 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4364 1.34 - 1.46: 3605 1.46 - 1.58: 7256 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 15309 Sorted by residual: bond pdb=" C LEU D 312 " pdb=" N PRO D 313 " ideal model delta sigma weight residual 1.335 1.379 -0.044 9.40e-03 1.13e+04 2.19e+01 bond pdb=" C LEU G 312 " pdb=" N PRO G 313 " ideal model delta sigma weight residual 1.335 1.379 -0.044 9.40e-03 1.13e+04 2.17e+01 bond pdb=" C LEU E 312 " pdb=" N PRO E 313 " ideal model delta sigma weight residual 1.335 1.379 -0.044 9.40e-03 1.13e+04 2.17e+01 bond pdb=" C LEU F 312 " pdb=" N PRO F 313 " ideal model delta sigma weight residual 1.335 1.378 -0.043 9.40e-03 1.13e+04 2.10e+01 bond pdb=" C LEU C 312 " pdb=" N PRO C 313 " ideal model delta sigma weight residual 1.335 1.378 -0.043 9.40e-03 1.13e+04 2.10e+01 ... (remaining 15304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 19477 1.73 - 3.47: 1027 3.47 - 5.20: 196 5.20 - 6.94: 86 6.94 - 8.67: 39 Bond angle restraints: 20825 Sorted by residual: angle pdb=" N ILE A 268 " pdb=" CA ILE A 268 " pdb=" CB ILE A 268 " ideal model delta sigma weight residual 112.33 107.01 5.32 1.19e+00 7.06e-01 2.00e+01 angle pdb=" N ILE G 268 " pdb=" CA ILE G 268 " pdb=" CB ILE G 268 " ideal model delta sigma weight residual 112.33 107.02 5.31 1.19e+00 7.06e-01 1.99e+01 angle pdb=" N ILE C 268 " pdb=" CA ILE C 268 " pdb=" CB ILE C 268 " ideal model delta sigma weight residual 112.33 107.03 5.30 1.19e+00 7.06e-01 1.99e+01 angle pdb=" N ILE F 268 " pdb=" CA ILE F 268 " pdb=" CB ILE F 268 " ideal model delta sigma weight residual 112.33 107.03 5.30 1.19e+00 7.06e-01 1.99e+01 angle pdb=" N ILE E 268 " pdb=" CA ILE E 268 " pdb=" CB ILE E 268 " ideal model delta sigma weight residual 112.33 107.03 5.30 1.19e+00 7.06e-01 1.98e+01 ... (remaining 20820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.28: 6935 10.28 - 20.57: 1311 20.57 - 30.85: 573 30.85 - 41.13: 211 41.13 - 51.42: 84 Dihedral angle restraints: 9114 sinusoidal: 3563 harmonic: 5551 Sorted by residual: dihedral pdb=" CA VAL D 308 " pdb=" C VAL D 308 " pdb=" N TYR D 309 " pdb=" CA TYR D 309 " ideal model delta harmonic sigma weight residual -180.00 -156.13 -23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA VAL G 308 " pdb=" C VAL G 308 " pdb=" N TYR G 309 " pdb=" CA TYR G 309 " ideal model delta harmonic sigma weight residual 180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA VAL E 308 " pdb=" C VAL E 308 " pdb=" N TYR E 309 " pdb=" CA TYR E 309 " ideal model delta harmonic sigma weight residual -180.00 -156.21 -23.79 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 9111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1242 0.036 - 0.072: 792 0.072 - 0.107: 274 0.107 - 0.143: 111 0.143 - 0.179: 52 Chirality restraints: 2471 Sorted by residual: chirality pdb=" CA LEU A 101 " pdb=" N LEU A 101 " pdb=" C LEU A 101 " pdb=" CB LEU A 101 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CA LEU B 101 " pdb=" N LEU B 101 " pdb=" C LEU B 101 " pdb=" CB LEU B 101 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA LEU G 101 " pdb=" N LEU G 101 " pdb=" C LEU G 101 " pdb=" CB LEU G 101 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 2468 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 123 " -0.054 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO C 124 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 124 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 124 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 123 " 0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO A 124 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 123 " 0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO G 124 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO G 124 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 124 " 0.046 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 752 2.72 - 3.27: 15541 3.27 - 3.81: 24514 3.81 - 4.36: 29248 4.36 - 4.90: 44640 Nonbonded interactions: 114695 Sorted by model distance: nonbonded pdb=" O PHE F 72 " pdb=" OG SER G 71 " model vdw 2.175 3.040 nonbonded pdb=" O PHE A 72 " pdb=" OG SER B 71 " model vdw 2.224 3.040 nonbonded pdb=" O PHE E 72 " pdb=" OG SER F 71 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 71 " pdb=" O PHE G 72 " model vdw 2.285 3.040 nonbonded pdb=" O GLU A 310 " pdb=" OG1 THR A 314 " model vdw 2.293 3.040 ... (remaining 114690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 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 Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 11.700 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15323 Z= 0.261 Angle : 0.997 8.669 20853 Z= 0.550 Chirality : 0.055 0.179 2471 Planarity : 0.009 0.081 2520 Dihedral : 14.609 48.948 5460 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.56 (0.13), residues: 1827 helix: -3.55 (0.09), residues: 1183 sheet: None (None), residues: 0 loop : -3.65 (0.18), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 217 TYR 0.017 0.002 TYR B 284 PHE 0.012 0.002 PHE B 263 TRP 0.011 0.002 TRP B 104 HIS 0.008 0.002 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00501 (15309) covalent geometry : angle 0.99801 (20825) SS BOND : bond 0.00182 ( 14) SS BOND : angle 0.40798 ( 28) hydrogen bonds : bond 0.30695 ( 645) hydrogen bonds : angle 9.69477 ( 1893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.9377 (tpp-160) cc_final: 0.8564 (mpt180) REVERT: A 121 TYR cc_start: 0.9284 (t80) cc_final: 0.9078 (t80) REVERT: A 205 ASN cc_start: 0.9455 (p0) cc_final: 0.9252 (p0) REVERT: A 318 LEU cc_start: 0.8607 (tt) cc_final: 0.8318 (mt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0758 time to fit residues: 5.2608 Evaluate side-chains 34 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.0170 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0170 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0270 chunk 91 optimal weight: 0.0010 chunk 149 optimal weight: 6.9990 overall best weight: 0.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.066742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.052761 restraints weight = 15054.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.054126 restraints weight = 9065.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.055052 restraints weight = 6352.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.055642 restraints weight = 4943.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.055930 restraints weight = 4185.739| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15323 Z= 0.147 Angle : 0.822 10.165 20853 Z= 0.413 Chirality : 0.048 0.203 2471 Planarity : 0.007 0.051 2520 Dihedral : 6.427 24.961 1981 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.17), residues: 1827 helix: -1.78 (0.13), residues: 1176 sheet: None (None), residues: 0 loop : -3.40 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG G 254 TYR 0.014 0.001 TYR C 111 PHE 0.020 0.002 PHE E 141 TRP 0.009 0.001 TRP G 104 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00289 (15309) covalent geometry : angle 0.82045 (20825) SS BOND : bond 0.01007 ( 14) SS BOND : angle 1.61801 ( 28) hydrogen bonds : bond 0.04799 ( 645) hydrogen bonds : angle 5.60247 ( 1893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.8901 (ttt) cc_final: 0.8589 (ttp) REVERT: A 75 ARG cc_start: 0.9344 (tpp-160) cc_final: 0.8414 (mtt90) REVERT: A 121 TYR cc_start: 0.9443 (t80) cc_final: 0.9205 (t80) REVERT: A 141 PHE cc_start: 0.9248 (t80) cc_final: 0.8996 (t80) REVERT: A 145 GLU cc_start: 0.9560 (mt-10) cc_final: 0.9255 (mt-10) REVERT: A 205 ASN cc_start: 0.9425 (p0) cc_final: 0.9180 (p0) REVERT: A 273 PHE cc_start: 0.9226 (m-10) cc_final: 0.8694 (m-80) REVERT: A 331 TYR cc_start: 0.7998 (t80) cc_final: 0.7290 (m-10) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0617 time to fit residues: 4.0674 Evaluate side-chains 35 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 116 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 158 optimal weight: 0.0370 chunk 26 optimal weight: 10.0000 chunk 68 optimal weight: 0.0770 chunk 129 optimal weight: 0.6980 chunk 125 optimal weight: 0.0970 chunk 141 optimal weight: 0.0270 chunk 165 optimal weight: 4.9990 chunk 100 optimal weight: 0.0670 overall best weight: 0.0610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.067852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.054345 restraints weight = 15536.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.055743 restraints weight = 9552.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.056650 restraints weight = 6788.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.057326 restraints weight = 5365.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.057722 restraints weight = 4513.722| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15323 Z= 0.140 Angle : 0.767 7.198 20853 Z= 0.381 Chirality : 0.046 0.172 2471 Planarity : 0.005 0.045 2520 Dihedral : 5.901 24.585 1981 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.41 % Allowed : 3.73 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.19), residues: 1827 helix: -1.17 (0.15), residues: 1141 sheet: -1.07 (0.60), residues: 84 loop : -2.80 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 254 TYR 0.012 0.001 TYR A 325 PHE 0.009 0.001 PHE G 67 TRP 0.008 0.001 TRP D 104 HIS 0.004 0.001 HIS G 319 Details of bonding type rmsd covalent geometry : bond 0.00287 (15309) covalent geometry : angle 0.76563 (20825) SS BOND : bond 0.00948 ( 14) SS BOND : angle 1.52606 ( 28) hydrogen bonds : bond 0.04187 ( 645) hydrogen bonds : angle 5.14380 ( 1893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8696 (ttt) cc_final: 0.8441 (ttp) REVERT: A 75 ARG cc_start: 0.9325 (tpp-160) cc_final: 0.8649 (mpt180) REVERT: A 141 PHE cc_start: 0.9258 (t80) cc_final: 0.9039 (t80) REVERT: A 145 GLU cc_start: 0.9590 (mt-10) cc_final: 0.9247 (mt-10) REVERT: A 205 ASN cc_start: 0.9412 (p0) cc_final: 0.9191 (p0) REVERT: A 267 LEU cc_start: 0.9412 (tp) cc_final: 0.9193 (tp) REVERT: A 273 PHE cc_start: 0.9187 (m-10) cc_final: 0.8697 (m-80) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.0609 time to fit residues: 3.7091 Evaluate side-chains 32 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 168 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 161 optimal weight: 0.0000 chunk 24 optimal weight: 0.0170 chunk 128 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 overall best weight: 0.8424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.067543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.054124 restraints weight = 15857.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.055490 restraints weight = 10072.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.056362 restraints weight = 7244.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.057032 restraints weight = 5747.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.057463 restraints weight = 4846.633| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15323 Z= 0.123 Angle : 0.747 7.089 20853 Z= 0.367 Chirality : 0.046 0.155 2471 Planarity : 0.005 0.044 2520 Dihedral : 5.495 22.954 1981 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.19), residues: 1827 helix: -0.53 (0.16), residues: 1092 sheet: -1.20 (0.54), residues: 84 loop : -2.85 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 254 TYR 0.012 0.001 TYR G 121 PHE 0.006 0.001 PHE E 141 TRP 0.015 0.001 TRP E 127 HIS 0.002 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00256 (15309) covalent geometry : angle 0.74572 (20825) SS BOND : bond 0.00119 ( 14) SS BOND : angle 1.47450 ( 28) hydrogen bonds : bond 0.03622 ( 645) hydrogen bonds : angle 4.80686 ( 1893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8877 (ttt) cc_final: 0.8617 (ttp) REVERT: A 75 ARG cc_start: 0.9383 (tpp-160) cc_final: 0.8651 (mpt180) REVERT: A 121 TYR cc_start: 0.9199 (t80) cc_final: 0.8988 (t80) REVERT: A 267 LEU cc_start: 0.9483 (tp) cc_final: 0.9271 (tp) REVERT: A 273 PHE cc_start: 0.9301 (m-10) cc_final: 0.8712 (m-80) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0628 time to fit residues: 3.1146 Evaluate side-chains 28 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 154 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 97 optimal weight: 0.0770 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.065060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.051829 restraints weight = 15811.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.053132 restraints weight = 10065.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.054027 restraints weight = 7269.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054567 restraints weight = 5752.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.054984 restraints weight = 4908.817| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15323 Z= 0.145 Angle : 0.724 6.511 20853 Z= 0.363 Chirality : 0.045 0.142 2471 Planarity : 0.005 0.038 2520 Dihedral : 5.411 18.010 1981 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.20), residues: 1827 helix: -0.29 (0.15), residues: 1134 sheet: -1.59 (0.55), residues: 84 loop : -2.76 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 217 TYR 0.009 0.001 TYR F 121 PHE 0.009 0.001 PHE G 235 TRP 0.010 0.002 TRP B 127 HIS 0.002 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00314 (15309) covalent geometry : angle 0.72224 (20825) SS BOND : bond 0.00444 ( 14) SS BOND : angle 1.50806 ( 28) hydrogen bonds : bond 0.03240 ( 645) hydrogen bonds : angle 4.65415 ( 1893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.9416 (tpp-160) cc_final: 0.8495 (mmt180) REVERT: A 273 PHE cc_start: 0.9370 (m-10) cc_final: 0.8850 (m-80) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0665 time to fit residues: 3.5007 Evaluate side-chains 29 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 31 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 132 optimal weight: 0.2980 chunk 116 optimal weight: 0.5980 chunk 138 optimal weight: 7.9990 chunk 177 optimal weight: 0.4980 chunk 134 optimal weight: 0.7980 chunk 45 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.066843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.053856 restraints weight = 15502.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.055205 restraints weight = 9762.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.056158 restraints weight = 7025.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.056790 restraints weight = 5544.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.057181 restraints weight = 4693.243| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15323 Z= 0.124 Angle : 0.727 6.615 20853 Z= 0.356 Chirality : 0.045 0.141 2471 Planarity : 0.005 0.038 2520 Dihedral : 5.334 21.247 1981 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.19), residues: 1827 helix: -0.18 (0.16), residues: 1092 sheet: -1.15 (0.47), residues: 84 loop : -2.78 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 217 TYR 0.008 0.001 TYR E 83 PHE 0.017 0.001 PHE D 54 TRP 0.008 0.001 TRP F 104 HIS 0.001 0.000 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00257 (15309) covalent geometry : angle 0.72677 (20825) SS BOND : bond 0.00589 ( 14) SS BOND : angle 0.75738 ( 28) hydrogen bonds : bond 0.03140 ( 645) hydrogen bonds : angle 4.66676 ( 1893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.9259 (tpp-160) cc_final: 0.8657 (mpt180) REVERT: A 273 PHE cc_start: 0.9169 (m-10) cc_final: 0.8683 (m-80) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0604 time to fit residues: 3.1398 Evaluate side-chains 27 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 83 optimal weight: 0.0970 chunk 169 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.065610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.052455 restraints weight = 15132.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.053824 restraints weight = 9699.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.054796 restraints weight = 6990.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.055412 restraints weight = 5473.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.055815 restraints weight = 4599.058| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15323 Z= 0.116 Angle : 0.702 7.407 20853 Z= 0.340 Chirality : 0.045 0.134 2471 Planarity : 0.005 0.040 2520 Dihedral : 5.125 20.012 1981 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.19), residues: 1827 helix: -0.17 (0.16), residues: 1127 sheet: 0.12 (0.51), residues: 70 loop : -2.75 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 217 TYR 0.007 0.001 TYR C 83 PHE 0.009 0.001 PHE E 129 TRP 0.013 0.001 TRP G 127 HIS 0.001 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00254 (15309) covalent geometry : angle 0.69948 (20825) SS BOND : bond 0.00664 ( 14) SS BOND : angle 1.73174 ( 28) hydrogen bonds : bond 0.02844 ( 645) hydrogen bonds : angle 4.28816 ( 1893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 273 PHE cc_start: 0.9149 (m-10) cc_final: 0.8664 (m-80) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0490 time to fit residues: 2.6487 Evaluate side-chains 26 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 68 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 57 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 60 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 157 optimal weight: 0.0270 chunk 77 optimal weight: 4.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.066770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.053170 restraints weight = 14813.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.054538 restraints weight = 9631.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.055500 restraints weight = 7025.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.056147 restraints weight = 5565.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.056601 restraints weight = 4690.399| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15323 Z= 0.114 Angle : 0.690 7.906 20853 Z= 0.332 Chirality : 0.045 0.130 2471 Planarity : 0.005 0.038 2520 Dihedral : 4.898 19.399 1981 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.19), residues: 1827 helix: -0.38 (0.15), residues: 1148 sheet: 0.44 (0.54), residues: 70 loop : -2.88 (0.22), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 217 TYR 0.005 0.001 TYR B 331 PHE 0.016 0.001 PHE A 141 TRP 0.011 0.001 TRP A 127 HIS 0.001 0.000 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00238 (15309) covalent geometry : angle 0.68947 (20825) SS BOND : bond 0.00757 ( 14) SS BOND : angle 0.78011 ( 28) hydrogen bonds : bond 0.02740 ( 645) hydrogen bonds : angle 4.25442 ( 1893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 ASP cc_start: 0.8671 (t70) cc_final: 0.8382 (t70) REVERT: B 141 PHE cc_start: 0.9103 (t80) cc_final: 0.8884 (t80) REVERT: B 284 TYR cc_start: 0.9138 (m-10) cc_final: 0.8642 (m-80) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0608 time to fit residues: 3.0992 Evaluate side-chains 30 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 21 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 24 optimal weight: 0.0670 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 0.0570 chunk 139 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 overall best weight: 1.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.066019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.052988 restraints weight = 15168.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.054281 restraints weight = 9549.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.055147 restraints weight = 7030.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.055688 restraints weight = 5542.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.056126 restraints weight = 4724.667| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15323 Z= 0.118 Angle : 0.684 7.386 20853 Z= 0.334 Chirality : 0.045 0.149 2471 Planarity : 0.005 0.039 2520 Dihedral : 4.888 17.547 1981 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.19), residues: 1827 helix: -0.34 (0.15), residues: 1141 sheet: 0.01 (0.51), residues: 70 loop : -2.92 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 217 TYR 0.006 0.001 TYR E 284 PHE 0.017 0.001 PHE A 141 TRP 0.013 0.001 TRP G 127 HIS 0.001 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00257 (15309) covalent geometry : angle 0.68290 (20825) SS BOND : bond 0.00597 ( 14) SS BOND : angle 1.20654 ( 28) hydrogen bonds : bond 0.02736 ( 645) hydrogen bonds : angle 4.07669 ( 1893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 ASP cc_start: 0.8680 (t70) cc_final: 0.8407 (t70) REVERT: B 141 PHE cc_start: 0.9121 (t80) cc_final: 0.8899 (t80) REVERT: B 280 ASN cc_start: 0.8742 (t160) cc_final: 0.8276 (t0) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0487 time to fit residues: 2.5666 Evaluate side-chains 28 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 35 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 28 optimal weight: 0.0970 chunk 96 optimal weight: 10.0000 chunk 116 optimal weight: 0.0370 chunk 37 optimal weight: 0.0040 chunk 120 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 179 optimal weight: 0.0010 overall best weight: 0.1074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.068296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.054499 restraints weight = 15225.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.056066 restraints weight = 9400.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.057083 restraints weight = 6614.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.057775 restraints weight = 5122.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.058199 restraints weight = 4278.181| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.6785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15323 Z= 0.136 Angle : 0.744 7.608 20853 Z= 0.367 Chirality : 0.047 0.250 2471 Planarity : 0.005 0.039 2520 Dihedral : 4.814 20.728 1981 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.19), residues: 1827 helix: -0.37 (0.15), residues: 1127 sheet: None (None), residues: 0 loop : -2.90 (0.19), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 217 TYR 0.015 0.001 TYR D 325 PHE 0.019 0.001 PHE A 54 TRP 0.009 0.001 TRP B 127 HIS 0.000 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00274 (15309) covalent geometry : angle 0.74181 (20825) SS BOND : bond 0.00886 ( 14) SS BOND : angle 1.75085 ( 28) hydrogen bonds : bond 0.04068 ( 645) hydrogen bonds : angle 4.11734 ( 1893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 PHE cc_start: 0.9098 (t80) cc_final: 0.8886 (t80) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0491 time to fit residues: 2.6376 Evaluate side-chains 27 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 90 optimal weight: 0.3980 chunk 169 optimal weight: 0.7980 chunk 159 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 22 optimal weight: 0.0270 chunk 48 optimal weight: 0.0270 chunk 136 optimal weight: 0.0000 chunk 15 optimal weight: 5.9990 chunk 80 optimal weight: 0.0170 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.0060 overall best weight: 0.0154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.068550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.054578 restraints weight = 15144.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.056098 restraints weight = 9480.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.057164 restraints weight = 6708.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.057871 restraints weight = 5230.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.058340 restraints weight = 4380.260| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15323 Z= 0.120 Angle : 0.705 7.570 20853 Z= 0.335 Chirality : 0.045 0.127 2471 Planarity : 0.005 0.038 2520 Dihedral : 4.597 19.674 1981 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.19), residues: 1827 helix: -0.05 (0.16), residues: 1141 sheet: None (None), residues: 0 loop : -2.84 (0.19), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 217 TYR 0.017 0.001 TYR B 284 PHE 0.014 0.001 PHE A 141 TRP 0.008 0.001 TRP D 127 HIS 0.000 0.000 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00240 (15309) covalent geometry : angle 0.70374 (20825) SS BOND : bond 0.00684 ( 14) SS BOND : angle 1.51935 ( 28) hydrogen bonds : bond 0.02590 ( 645) hydrogen bonds : angle 3.90333 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1175.86 seconds wall clock time: 21 minutes 34.55 seconds (1294.55 seconds total)