Starting phenix.real_space_refine on Tue Dec 31 06:16:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m68_30116/12_2024/6m68_30116.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m68_30116/12_2024/6m68_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6m68_30116/12_2024/6m68_30116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m68_30116/12_2024/6m68_30116.map" model { file = "/net/cci-nas-00/data/ceres_data/6m68_30116/12_2024/6m68_30116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m68_30116/12_2024/6m68_30116.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.028 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: C, B, E, D, G, F Time building chain proxies: 5.30, per 1000 atoms: 0.35 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=2, 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 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: 3.56 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.37 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: 3.50 Time building geometry restraints manager: 4.10 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: 6923 10.28 - 20.57: 1305 20.57 - 30.85: 567 30.85 - 41.13: 205 41.13 - 51.42: 78 Dihedral angle restraints: 9078 sinusoidal: 3527 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 9075 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: 2.03 - 2.60: 177 2.60 - 3.18: 12589 3.18 - 3.75: 24012 3.75 - 4.33: 31380 4.33 - 4.90: 46573 Nonbonded interactions: 114731 Sorted by model distance: nonbonded pdb=" SG CYS D 84 " pdb=" SG CYS D 246 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS G 84 " pdb=" SG CYS G 246 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS C 84 " pdb=" SG CYS C 246 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS E 84 " pdb=" SG CYS E 246 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS F 84 " pdb=" SG CYS F 246 " model vdw 2.029 3.760 ... (remaining 114726 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: 0.00 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 28.470 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.280 ------------------------------------------------------------------------------- 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 15309 Z= 0.323 Angle : 0.998 8.669 20825 Z= 0.551 Chirality : 0.055 0.179 2471 Planarity : 0.009 0.081 2520 Dihedral : 14.609 48.948 5460 Min Nonbonded Distance : 2.028 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.002 TRP B 104 HIS 0.008 0.002 HIS F 106 PHE 0.012 0.002 PHE B 263 TYR 0.017 0.002 TYR B 284 ARG 0.004 0.001 ARG C 217 *********************** 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 : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.9376 (tpp-160) cc_final: 0.8564 (mpt180) REVERT: A 121 TYR cc_start: 0.9283 (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: 0.8608 (tt) cc_final: 0.8318 (mt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2122 time to fit residues: 14.9236 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 : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 47 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15309 Z= 0.181 Angle : 0.806 7.968 20825 Z= 0.408 Chirality : 0.048 0.205 2471 Planarity : 0.006 0.053 2520 Dihedral : 6.413 23.606 1981 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.17), residues: 1827 helix: -1.65 (0.13), residues: 1169 sheet: None (None), residues: 0 loop : -3.40 (0.20), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.001 0.000 HIS A 319 PHE 0.022 0.002 PHE C 141 TYR 0.015 0.001 TYR G 111 ARG 0.004 0.001 ARG C 254 *********************** 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 : 0.265 Fit side-chains REVERT: A 37 MET cc_start: 0.8978 (ttt) cc_final: 0.8702 (ttp) REVERT: A 75 ARG cc_start: 0.9273 (tpp-160) cc_final: 0.8373 (mtt90) REVERT: A 121 TYR cc_start: 0.9401 (t80) cc_final: 0.9157 (t80) REVERT: A 141 PHE cc_start: 0.9296 (t80) cc_final: 0.9043 (t80) REVERT: A 145 GLU cc_start: 0.9558 (mt-10) cc_final: 0.9259 (mt-10) REVERT: A 205 ASN cc_start: 0.9451 (p0) cc_final: 0.9243 (p0) REVERT: A 273 PHE cc_start: 0.9164 (m-10) cc_final: 0.8622 (m-80) REVERT: A 331 TYR cc_start: 0.8001 (t80) cc_final: 0.7313 (m-10) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1401 time to fit residues: 9.2454 Evaluate side-chains 31 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 20.0000 chunk 51 optimal weight: 0.0770 chunk 137 optimal weight: 5.9990 chunk 112 optimal weight: 0.3980 chunk 45 optimal weight: 0.0170 chunk 165 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 164 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15309 Z= 0.176 Angle : 0.759 8.270 20825 Z= 0.380 Chirality : 0.047 0.175 2471 Planarity : 0.005 0.045 2520 Dihedral : 5.880 22.266 1981 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.18), residues: 1827 helix: -1.02 (0.15), residues: 1141 sheet: None (None), residues: 0 loop : -2.75 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 104 HIS 0.005 0.001 HIS C 319 PHE 0.007 0.001 PHE B 67 TYR 0.012 0.001 TYR D 325 ARG 0.005 0.001 ARG C 254 *********************** REFINEMENT MACRO_CYCLE 3 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 45 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 TYR cc_start: 0.9382 (t80) cc_final: 0.9158 (t80) REVERT: D 145 GLU cc_start: 0.9600 (mt-10) cc_final: 0.9248 (mt-10) REVERT: D 273 PHE cc_start: 0.9025 (m-10) cc_final: 0.8615 (m-80) outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.1427 time to fit residues: 7.6225 Evaluate side-chains 25 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 157 optimal weight: 5.9990 chunk 47 optimal weight: 0.0970 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15309 Z= 0.185 Angle : 0.720 6.406 20825 Z= 0.357 Chirality : 0.045 0.152 2471 Planarity : 0.005 0.044 2520 Dihedral : 5.475 21.695 1981 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.19), residues: 1827 helix: -0.88 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -2.94 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 127 HIS 0.002 0.001 HIS B 106 PHE 0.012 0.001 PHE A 141 TYR 0.008 0.001 TYR F 325 ARG 0.004 0.001 ARG G 217 *********************** REFINEMENT MACRO_CYCLE 4 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 40 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 TYR cc_start: 0.9431 (t80) cc_final: 0.9193 (t80) REVERT: D 125 LEU cc_start: 0.9743 (tp) cc_final: 0.9286 (pp) REVERT: D 141 PHE cc_start: 0.9195 (t80) cc_final: 0.8925 (t80) REVERT: D 145 GLU cc_start: 0.9588 (mt-10) cc_final: 0.9291 (mt-10) REVERT: D 273 PHE cc_start: 0.9115 (m-10) cc_final: 0.8630 (m-80) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1554 time to fit residues: 7.4304 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 : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.7980 chunk 99 optimal weight: 0.0170 chunk 2 optimal weight: 0.4980 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 overall best weight: 1.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15309 Z= 0.167 Angle : 0.691 6.381 20825 Z= 0.346 Chirality : 0.045 0.143 2471 Planarity : 0.005 0.044 2520 Dihedral : 5.266 16.275 1981 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 12.87 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.19), residues: 1827 helix: -0.57 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -2.54 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 127 HIS 0.001 0.000 HIS B 106 PHE 0.021 0.001 PHE D 54 TYR 0.009 0.001 TYR C 83 ARG 0.003 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 5 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 42 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 TYR cc_start: 0.9459 (t80) cc_final: 0.9195 (t80) REVERT: D 125 LEU cc_start: 0.9768 (tp) cc_final: 0.9299 (pp) REVERT: D 141 PHE cc_start: 0.9156 (t80) cc_final: 0.8875 (t80) REVERT: D 145 GLU cc_start: 0.9538 (mt-10) cc_final: 0.9197 (mt-10) REVERT: D 273 PHE cc_start: 0.9124 (m-10) cc_final: 0.8770 (m-80) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1350 time to fit residues: 6.8804 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 : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 34 optimal weight: 0.0770 chunk 103 optimal weight: 0.0040 chunk 43 optimal weight: 20.0000 chunk 176 optimal weight: 5.9990 chunk 146 optimal weight: 0.0670 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.8292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15309 Z= 0.158 Angle : 0.678 6.186 20825 Z= 0.332 Chirality : 0.044 0.137 2471 Planarity : 0.005 0.041 2520 Dihedral : 4.912 19.919 1981 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1827 helix: -0.05 (0.16), residues: 1113 sheet: None (None), residues: 0 loop : -2.15 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.001 0.000 HIS C 134 PHE 0.013 0.001 PHE D 54 TYR 0.009 0.001 TYR E 83 ARG 0.005 0.001 ARG E 217 *********************** REFINEMENT MACRO_CYCLE 6 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 46 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 125 LEU cc_start: 0.9782 (tp) cc_final: 0.9433 (pp) REVERT: D 141 PHE cc_start: 0.9145 (t80) cc_final: 0.8866 (t80) REVERT: D 145 GLU cc_start: 0.9548 (mt-10) cc_final: 0.9223 (mt-10) REVERT: D 273 PHE cc_start: 0.9119 (m-10) cc_final: 0.8793 (m-80) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1265 time to fit residues: 7.1163 Evaluate side-chains 33 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 100 optimal weight: 0.0000 chunk 128 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 98 optimal weight: 0.0870 chunk 175 optimal weight: 4.9990 chunk 109 optimal weight: 0.0010 chunk 106 optimal weight: 5.9990 chunk 80 optimal weight: 0.3980 overall best weight: 0.2368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15309 Z= 0.149 Angle : 0.676 6.538 20825 Z= 0.325 Chirality : 0.043 0.127 2471 Planarity : 0.005 0.041 2520 Dihedral : 4.743 17.638 1981 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1827 helix: 0.34 (0.17), residues: 1064 sheet: -0.91 (0.61), residues: 70 loop : -2.14 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 104 HIS 0.001 0.000 HIS G 106 PHE 0.011 0.001 PHE D 54 TYR 0.007 0.001 TYR C 83 ARG 0.004 0.000 ARG C 217 *********************** 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 : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 125 LEU cc_start: 0.9785 (tp) cc_final: 0.9457 (pp) REVERT: D 273 PHE cc_start: 0.9024 (m-10) cc_final: 0.8695 (m-80) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1237 time to fit residues: 6.6645 Evaluate side-chains 33 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 16 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15309 Z= 0.143 Angle : 0.647 6.535 20825 Z= 0.310 Chirality : 0.043 0.132 2471 Planarity : 0.005 0.040 2520 Dihedral : 4.547 17.034 1981 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.20), residues: 1827 helix: 0.25 (0.17), residues: 1106 sheet: None (None), residues: 0 loop : -2.35 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 127 HIS 0.001 0.000 HIS G 106 PHE 0.012 0.001 PHE D 54 TYR 0.007 0.001 TYR A 83 ARG 0.003 0.000 ARG C 217 *********************** 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 41 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 ASP cc_start: 0.8670 (t70) cc_final: 0.8436 (t70) REVERT: D 125 LEU cc_start: 0.9796 (tp) cc_final: 0.9468 (pp) REVERT: D 273 PHE cc_start: 0.9009 (m-10) cc_final: 0.8687 (m-80) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1230 time to fit residues: 6.1749 Evaluate side-chains 31 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 153 optimal weight: 0.0170 chunk 163 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 0.1980 chunk 128 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 154 optimal weight: 0.3980 chunk 162 optimal weight: 0.0670 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.6604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15309 Z= 0.144 Angle : 0.668 6.654 20825 Z= 0.321 Chirality : 0.045 0.177 2471 Planarity : 0.005 0.039 2520 Dihedral : 4.673 21.176 1981 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1827 helix: 0.09 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -2.50 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 85 HIS 0.000 0.000 HIS D 106 PHE 0.015 0.001 PHE E 109 TYR 0.005 0.001 TYR E 325 ARG 0.004 0.001 ARG E 217 *********************** 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 41 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 125 LEU cc_start: 0.9790 (tp) cc_final: 0.9533 (mt) REVERT: D 273 PHE cc_start: 0.8995 (m-10) cc_final: 0.8620 (m-80) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1294 time to fit residues: 6.4295 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 : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.5980 chunk 172 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 181 optimal weight: 0.3980 chunk 166 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.6659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15309 Z= 0.161 Angle : 0.655 6.503 20825 Z= 0.320 Chirality : 0.046 0.139 2471 Planarity : 0.005 0.039 2520 Dihedral : 4.680 20.716 1981 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1827 helix: 0.22 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -2.45 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 127 HIS 0.001 0.001 HIS G 106 PHE 0.016 0.001 PHE B 109 TYR 0.005 0.001 TYR A 111 ARG 0.003 0.000 ARG F 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 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 : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.8738 (ttp) cc_final: 0.8469 (tmm) REVERT: B 122 LEU cc_start: 0.9824 (mt) cc_final: 0.9514 (tt) REVERT: B 125 LEU cc_start: 0.9772 (tp) cc_final: 0.9407 (pp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1307 time to fit residues: 6.7108 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 : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 5.9990 chunk 153 optimal weight: 0.1980 chunk 44 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 148 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.064113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.050244 restraints weight = 15975.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.051595 restraints weight = 10441.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.052488 restraints weight = 7676.536| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.6707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15309 Z= 0.201 Angle : 0.698 6.571 20825 Z= 0.343 Chirality : 0.045 0.135 2471 Planarity : 0.005 0.038 2520 Dihedral : 4.826 19.135 1981 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 13.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.19), residues: 1827 helix: -0.26 (0.15), residues: 1197 sheet: None (None), residues: 0 loop : -2.44 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 85 HIS 0.003 0.001 HIS A 319 PHE 0.017 0.001 PHE A 54 TYR 0.011 0.001 TYR D 331 ARG 0.003 0.000 ARG F 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2075.13 seconds wall clock time: 39 minutes 40.42 seconds (2380.42 seconds total)