Starting phenix.real_space_refine on Thu Mar 5 14:28:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dwb_30880/03_2026/7dwb_30880.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dwb_30880/03_2026/7dwb_30880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dwb_30880/03_2026/7dwb_30880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dwb_30880/03_2026/7dwb_30880.map" model { file = "/net/cci-nas-00/data/ceres_data/7dwb_30880/03_2026/7dwb_30880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dwb_30880/03_2026/7dwb_30880.cif" } resolution = 3.15 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= 0.034 sd= 0.155 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 140 5.16 5 C 15323 2.51 5 N 3745 2.21 5 O 4256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23464 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3352 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 3.68, per 1000 atoms: 0.16 Number of scatterers: 23464 At special positions: 0 Unit cell: (119.88, 120.96, 137.16, 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 140 16.00 O 4256 8.00 N 3745 7.00 C 15323 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 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 273 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 273 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 273 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 273 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 254 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 254 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 254 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 254 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 254 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 254 " 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: 1.88 Conformation dependent library (CDL) restraints added in 868.7 milliseconds 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5656 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 7 sheets defined 53.7% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.558A pdb=" N LEU A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 62 Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.985A pdb=" N LEU A 105 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 120 removed outlier: 3.502A pdb=" N LEU A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 160 removed outlier: 4.072A pdb=" N ALA A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Proline residue: A 133 - end of helix removed outlier: 3.526A pdb=" N SER A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 138 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 154 " --> pdb=" O TYR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 164 removed outlier: 3.680A pdb=" N ASP A 164 " --> pdb=" O ARG A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 202 through 211 removed outlier: 4.133A pdb=" N GLN A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 247 removed outlier: 3.785A pdb=" N CYS A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 264 removed outlier: 4.174A pdb=" N ASN A 263 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 302 removed outlier: 3.532A pdb=" N LEU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.204A pdb=" N VAL A 316 " --> pdb=" O VAL A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.886A pdb=" N LYS A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.789A pdb=" N LYS A 363 " --> pdb=" O GLU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 381 removed outlier: 4.101A pdb=" N MET A 380 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 381 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.548A pdb=" N GLU A 406 " --> pdb=" O GLN A 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.557A pdb=" N LEU B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 62 Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.985A pdb=" N LEU B 105 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 120 removed outlier: 3.502A pdb=" N LEU B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 160 removed outlier: 4.073A pdb=" N ALA B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Proline residue: B 133 - end of helix removed outlier: 3.527A pdb=" N SER B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 138 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP B 147 " --> pdb=" O MET B 143 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 154 " --> pdb=" O TYR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 164 removed outlier: 3.680A pdb=" N ASP B 164 " --> pdb=" O ARG B 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 161 through 164' Processing helix chain 'B' and resid 202 through 211 removed outlier: 4.133A pdb=" N GLN B 206 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 247 removed outlier: 3.785A pdb=" N CYS B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 4.173A pdb=" N ASN B 263 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 302 removed outlier: 3.532A pdb=" N LEU B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) Proline residue: B 297 - end of helix Processing helix chain 'B' and resid 313 through 318 removed outlier: 4.203A pdb=" N VAL B 316 " --> pdb=" O VAL B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 350 through 357 removed outlier: 3.886A pdb=" N LYS B 354 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 removed outlier: 3.789A pdb=" N LYS B 363 " --> pdb=" O GLU B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 381 removed outlier: 4.101A pdb=" N MET B 380 " --> pdb=" O ASN B 377 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.548A pdb=" N GLU B 406 " --> pdb=" O GLN B 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 13 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.558A pdb=" N LEU C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 62 Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.986A pdb=" N LEU C 105 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.501A pdb=" N LEU C 114 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 160 removed outlier: 4.072A pdb=" N ALA C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Proline residue: C 133 - end of helix removed outlier: 3.526A pdb=" N SER C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP C 138 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP C 147 " --> pdb=" O MET C 143 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 154 " --> pdb=" O TYR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 164 removed outlier: 3.681A pdb=" N ASP C 164 " --> pdb=" O ARG C 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 161 through 164' Processing helix chain 'C' and resid 202 through 211 removed outlier: 4.133A pdb=" N GLN C 206 " --> pdb=" O PRO C 202 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 247 removed outlier: 3.786A pdb=" N CYS C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 264 removed outlier: 4.173A pdb=" N ASN C 263 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 302 removed outlier: 3.531A pdb=" N LEU C 283 " --> pdb=" O GLY C 279 " (cutoff:3.500A) Proline residue: C 297 - end of helix Processing helix chain 'C' and resid 313 through 318 removed outlier: 4.204A pdb=" N VAL C 316 " --> pdb=" O VAL C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 350 through 357 removed outlier: 3.886A pdb=" N LYS C 354 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 363 removed outlier: 3.789A pdb=" N LYS C 363 " --> pdb=" O GLU C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 381 removed outlier: 4.100A pdb=" N MET C 380 " --> pdb=" O ASN C 377 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE C 381 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.548A pdb=" N GLU C 406 " --> pdb=" O GLN C 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 13 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.558A pdb=" N LEU D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 62 Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.986A pdb=" N LEU D 105 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.502A pdb=" N LEU D 114 " --> pdb=" O PRO D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 160 removed outlier: 4.072A pdb=" N ALA D 132 " --> pdb=" O ARG D 128 " (cutoff:3.500A) Proline residue: D 133 - end of helix removed outlier: 3.527A pdb=" N SER D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP D 138 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP D 147 " --> pdb=" O MET D 143 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 164 removed outlier: 3.680A pdb=" N ASP D 164 " --> pdb=" O ARG D 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 164' Processing helix chain 'D' and resid 202 through 211 removed outlier: 4.133A pdb=" N GLN D 206 " --> pdb=" O PRO D 202 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 247 removed outlier: 3.785A pdb=" N CYS D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 removed outlier: 4.174A pdb=" N ASN D 263 " --> pdb=" O ILE D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 302 removed outlier: 3.532A pdb=" N LEU D 283 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Proline residue: D 297 - end of helix Processing helix chain 'D' and resid 313 through 318 removed outlier: 4.204A pdb=" N VAL D 316 " --> pdb=" O VAL D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 347 Processing helix chain 'D' and resid 350 through 357 removed outlier: 3.886A pdb=" N LYS D 354 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 363 removed outlier: 3.788A pdb=" N LYS D 363 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 381 removed outlier: 4.101A pdb=" N MET D 380 " --> pdb=" O ASN D 377 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 381 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 407 removed outlier: 3.548A pdb=" N GLU D 406 " --> pdb=" O GLN D 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.558A pdb=" N LEU E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 62 Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.985A pdb=" N LEU E 105 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 120 removed outlier: 3.501A pdb=" N LEU E 114 " --> pdb=" O PRO E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 160 removed outlier: 4.072A pdb=" N ALA E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Proline residue: E 133 - end of helix removed outlier: 3.526A pdb=" N SER E 137 " --> pdb=" O PRO E 133 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP E 138 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP E 147 " --> pdb=" O MET E 143 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE E 154 " --> pdb=" O TYR E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 164 removed outlier: 3.680A pdb=" N ASP E 164 " --> pdb=" O ARG E 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'E' and resid 202 through 211 removed outlier: 4.134A pdb=" N GLN E 206 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 247 removed outlier: 3.785A pdb=" N CYS E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 264 removed outlier: 4.174A pdb=" N ASN E 263 " --> pdb=" O ILE E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 302 removed outlier: 3.533A pdb=" N LEU E 283 " --> pdb=" O GLY E 279 " (cutoff:3.500A) Proline residue: E 297 - end of helix Processing helix chain 'E' and resid 313 through 318 removed outlier: 4.203A pdb=" N VAL E 316 " --> pdb=" O VAL E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 347 Processing helix chain 'E' and resid 350 through 357 removed outlier: 3.886A pdb=" N LYS E 354 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 363 removed outlier: 3.788A pdb=" N LYS E 363 " --> pdb=" O GLU E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 381 removed outlier: 4.101A pdb=" N MET E 380 " --> pdb=" O ASN E 377 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE E 381 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 407 removed outlier: 3.549A pdb=" N GLU E 406 " --> pdb=" O GLN E 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 13 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.557A pdb=" N LEU F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 62 Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.985A pdb=" N LEU F 105 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 120 removed outlier: 3.502A pdb=" N LEU F 114 " --> pdb=" O PRO F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 160 removed outlier: 4.072A pdb=" N ALA F 132 " --> pdb=" O ARG F 128 " (cutoff:3.500A) Proline residue: F 133 - end of helix removed outlier: 3.527A pdb=" N SER F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP F 138 " --> pdb=" O HIS F 134 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP F 147 " --> pdb=" O MET F 143 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS F 148 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE F 154 " --> pdb=" O TYR F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 164 removed outlier: 3.680A pdb=" N ASP F 164 " --> pdb=" O ARG F 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 161 through 164' Processing helix chain 'F' and resid 202 through 211 removed outlier: 4.133A pdb=" N GLN F 206 " --> pdb=" O PRO F 202 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 247 removed outlier: 3.785A pdb=" N CYS F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 264 removed outlier: 4.174A pdb=" N ASN F 263 " --> pdb=" O ILE F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 302 removed outlier: 3.531A pdb=" N LEU F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Proline residue: F 297 - end of helix Processing helix chain 'F' and resid 313 through 318 removed outlier: 4.203A pdb=" N VAL F 316 " --> pdb=" O VAL F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 347 Processing helix chain 'F' and resid 350 through 357 removed outlier: 3.886A pdb=" N LYS F 354 " --> pdb=" O VAL F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 363 removed outlier: 3.789A pdb=" N LYS F 363 " --> pdb=" O GLU F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 381 removed outlier: 4.101A pdb=" N MET F 380 " --> pdb=" O ASN F 377 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE F 381 " --> pdb=" O LEU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 407 removed outlier: 3.548A pdb=" N GLU F 406 " --> pdb=" O GLN F 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 13 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.557A pdb=" N LEU G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 62 Processing helix chain 'G' and resid 73 through 87 Processing helix chain 'G' and resid 102 through 106 removed outlier: 3.986A pdb=" N LEU G 105 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 120 removed outlier: 3.502A pdb=" N LEU G 114 " --> pdb=" O PRO G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 160 removed outlier: 4.072A pdb=" N ALA G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) Proline residue: G 133 - end of helix removed outlier: 3.527A pdb=" N SER G 137 " --> pdb=" O PRO G 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP G 138 " --> pdb=" O HIS G 134 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP G 147 " --> pdb=" O MET G 143 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS G 148 " --> pdb=" O GLU G 144 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE G 154 " --> pdb=" O TYR G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 164 removed outlier: 3.680A pdb=" N ASP G 164 " --> pdb=" O ARG G 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 161 through 164' Processing helix chain 'G' and resid 202 through 211 removed outlier: 4.133A pdb=" N GLN G 206 " --> pdb=" O PRO G 202 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 247 removed outlier: 3.785A pdb=" N CYS G 224 " --> pdb=" O LYS G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 264 removed outlier: 4.174A pdb=" N ASN G 263 " --> pdb=" O ILE G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 302 removed outlier: 3.532A pdb=" N LEU G 283 " --> pdb=" O GLY G 279 " (cutoff:3.500A) Proline residue: G 297 - end of helix Processing helix chain 'G' and resid 313 through 318 removed outlier: 4.203A pdb=" N VAL G 316 " --> pdb=" O VAL G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 347 Processing helix chain 'G' and resid 350 through 357 removed outlier: 3.886A pdb=" N LYS G 354 " --> pdb=" O VAL G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 363 removed outlier: 3.789A pdb=" N LYS G 363 " --> pdb=" O GLU G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 381 removed outlier: 4.101A pdb=" N MET G 380 " --> pdb=" O ASN G 377 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE G 381 " --> pdb=" O LEU G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 403 through 407 removed outlier: 3.548A pdb=" N GLU G 406 " --> pdb=" O GLN G 403 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.329A pdb=" N GLN A 272 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 67 removed outlier: 4.330A pdb=" N GLN B 272 " --> pdb=" O PHE B 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 67 removed outlier: 4.330A pdb=" N GLN C 272 " --> pdb=" O PHE C 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 67 removed outlier: 4.330A pdb=" N GLN D 272 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 67 removed outlier: 4.330A pdb=" N GLN E 272 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 67 removed outlier: 4.329A pdb=" N GLN F 272 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 67 removed outlier: 4.329A pdb=" N GLN G 272 " --> pdb=" O PHE G 67 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2667 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: 3.02 Time building geometry restraints manager: 2.61 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: 7245 1.34 - 1.46: 5079 1.46 - 1.58: 11455 1.58 - 1.69: 7 1.69 - 1.81: 203 Bond restraints: 23989 Sorted by residual: bond pdb=" C VAL C 305 " pdb=" N PRO C 306 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.18e+00 bond pdb=" C VAL D 305 " pdb=" N PRO D 306 " ideal model delta sigma weight residual 1.334 1.375 -0.042 2.34e-02 1.83e+03 3.15e+00 bond pdb=" C VAL G 305 " pdb=" N PRO G 306 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.11e+00 bond pdb=" C VAL F 305 " pdb=" N PRO F 306 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.11e+00 bond pdb=" C VAL B 305 " pdb=" N PRO B 306 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.10e+00 ... (remaining 23984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 31449 1.46 - 2.91: 827 2.91 - 4.37: 169 4.37 - 5.83: 56 5.83 - 7.29: 28 Bond angle restraints: 32529 Sorted by residual: angle pdb=" N ARG B 166 " pdb=" CA ARG B 166 " pdb=" C ARG B 166 " ideal model delta sigma weight residual 114.56 109.68 4.88 1.27e+00 6.20e-01 1.48e+01 angle pdb=" N ARG C 166 " pdb=" CA ARG C 166 " pdb=" C ARG C 166 " ideal model delta sigma weight residual 114.56 109.69 4.87 1.27e+00 6.20e-01 1.47e+01 angle pdb=" N ARG D 166 " pdb=" CA ARG D 166 " pdb=" C ARG D 166 " ideal model delta sigma weight residual 114.56 109.70 4.86 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N ARG A 166 " pdb=" CA ARG A 166 " pdb=" C ARG A 166 " ideal model delta sigma weight residual 114.56 109.71 4.85 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N ARG G 166 " pdb=" CA ARG G 166 " pdb=" C ARG G 166 " ideal model delta sigma weight residual 114.56 109.72 4.84 1.27e+00 6.20e-01 1.46e+01 ... (remaining 32524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 12861 16.60 - 33.20: 1349 33.20 - 49.80: 238 49.80 - 66.40: 7 66.40 - 83.00: 35 Dihedral angle restraints: 14490 sinusoidal: 5782 harmonic: 8708 Sorted by residual: dihedral pdb=" CA HIS F 175 " pdb=" C HIS F 175 " pdb=" N PRO F 176 " pdb=" CA PRO F 176 " ideal model delta harmonic sigma weight residual 180.00 152.28 27.72 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA HIS B 175 " pdb=" C HIS B 175 " pdb=" N PRO B 176 " pdb=" CA PRO B 176 " ideal model delta harmonic sigma weight residual 180.00 152.29 27.71 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA HIS C 175 " pdb=" C HIS C 175 " pdb=" N PRO C 176 " pdb=" CA PRO C 176 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 14487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2260 0.031 - 0.062: 1099 0.062 - 0.093: 299 0.093 - 0.124: 87 0.124 - 0.155: 21 Chirality restraints: 3766 Sorted by residual: chirality pdb=" CA ARG F 428 " pdb=" N ARG F 428 " pdb=" C ARG F 428 " pdb=" CB ARG F 428 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA ARG C 428 " pdb=" N ARG C 428 " pdb=" C ARG C 428 " pdb=" CB ARG C 428 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA ARG E 428 " pdb=" N ARG E 428 " pdb=" C ARG E 428 " pdb=" CB ARG E 428 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 3763 not shown) Planarity restraints: 4046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 320 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO A 321 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 320 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO E 321 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 321 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 321 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 320 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO C 321 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 321 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 321 " 0.029 5.00e-02 4.00e+02 ... (remaining 4043 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1258 2.74 - 3.28: 24943 3.28 - 3.82: 36881 3.82 - 4.36: 42984 4.36 - 4.90: 73983 Nonbonded interactions: 180049 Sorted by model distance: nonbonded pdb=" O SER C 433 " pdb=" OG SER D 433 " model vdw 2.194 3.040 nonbonded pdb=" O GLU E 196 " pdb=" OG SER F 393 " model vdw 2.229 3.040 nonbonded pdb=" OG SER G 348 " pdb=" OE1 GLU G 349 " model vdw 2.255 3.040 nonbonded pdb=" OG SER B 348 " pdb=" OE1 GLU B 349 " model vdw 2.256 3.040 nonbonded pdb=" OG SER A 348 " pdb=" OE1 GLU A 349 " model vdw 2.256 3.040 ... (remaining 180044 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 No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.160 Find NCS groups from input model: 0.130 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24003 Z= 0.116 Angle : 0.622 7.285 32557 Z= 0.318 Chirality : 0.040 0.155 3766 Planarity : 0.004 0.051 4046 Dihedral : 14.172 83.002 8792 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.03 % Favored : 88.73 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -1.95 (0.15), residues: 2919 helix: 0.34 (0.14), residues: 1414 sheet: 1.23 (0.44), residues: 84 loop : -3.37 (0.15), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 262 TYR 0.007 0.001 TYR G 121 PHE 0.015 0.001 PHE G 307 TRP 0.006 0.001 TRP G 127 HIS 0.003 0.001 HIS F 5 Details of bonding type rmsd covalent geometry : bond 0.00263 (23989) covalent geometry : angle 0.62193 (32529) SS BOND : bond 0.00044 ( 14) SS BOND : angle 0.23720 ( 28) hydrogen bonds : bond 0.30942 ( 973) hydrogen bonds : angle 6.76340 ( 2667) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8093 (mm) cc_final: 0.7724 (mm) REVERT: A 344 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7446 (mt-10) REVERT: A 357 LYS cc_start: 0.8345 (mmmt) cc_final: 0.8110 (mmtt) REVERT: A 360 GLU cc_start: 0.7652 (pm20) cc_final: 0.7451 (pm20) REVERT: B 52 LEU cc_start: 0.8058 (mm) cc_final: 0.7698 (mm) REVERT: B 134 HIS cc_start: 0.7785 (m90) cc_final: 0.7509 (m-70) REVERT: B 351 LYS cc_start: 0.8052 (mppt) cc_final: 0.7684 (mmmt) REVERT: B 360 GLU cc_start: 0.7536 (pm20) cc_final: 0.7322 (pm20) REVERT: B 392 MET cc_start: 0.4481 (pmm) cc_final: 0.3231 (pmm) REVERT: C 360 GLU cc_start: 0.7512 (pm20) cc_final: 0.6881 (pm20) REVERT: C 392 MET cc_start: 0.4383 (pmm) cc_final: 0.3719 (tmm) REVERT: D 351 LYS cc_start: 0.7976 (mppt) cc_final: 0.7376 (mptt) REVERT: D 360 GLU cc_start: 0.7395 (pm20) cc_final: 0.7070 (pm20) REVERT: D 392 MET cc_start: 0.4353 (pmm) cc_final: 0.3351 (pmm) REVERT: E 52 LEU cc_start: 0.8205 (mm) cc_final: 0.7777 (mm) REVERT: E 349 GLU cc_start: 0.7458 (pm20) cc_final: 0.7250 (pm20) REVERT: E 351 LYS cc_start: 0.8048 (mppt) cc_final: 0.7462 (mptt) REVERT: E 360 GLU cc_start: 0.7504 (pm20) cc_final: 0.7241 (pm20) REVERT: E 392 MET cc_start: 0.4590 (pmm) cc_final: 0.3420 (pmm) REVERT: F 52 LEU cc_start: 0.8154 (mm) cc_final: 0.7733 (mm) REVERT: F 134 HIS cc_start: 0.7842 (m90) cc_final: 0.7584 (m-70) REVERT: G 52 LEU cc_start: 0.8042 (mm) cc_final: 0.7704 (mm) REVERT: G 351 LYS cc_start: 0.8047 (mppt) cc_final: 0.7584 (mmmt) REVERT: G 360 GLU cc_start: 0.7540 (pm20) cc_final: 0.7285 (pm20) REVERT: G 392 MET cc_start: 0.5018 (pmm) cc_final: 0.3599 (pmm) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1587 time to fit residues: 81.5119 Evaluate side-chains 206 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 0.0270 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.0010 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 40.0000 chunk 111 optimal weight: 7.9990 overall best weight: 0.6244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN C 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.237378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.161795 restraints weight = 27671.742| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 3.41 r_work: 0.3742 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24003 Z= 0.152 Angle : 0.674 5.986 32557 Z= 0.348 Chirality : 0.042 0.149 3766 Planarity : 0.005 0.048 4046 Dihedral : 6.385 81.758 3143 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.31 % Favored : 89.45 % Rotamer: Outliers : 1.22 % Allowed : 8.02 % Favored : 90.77 % 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 (0.16), residues: 2919 helix: 0.82 (0.15), residues: 1386 sheet: 0.75 (0.47), residues: 84 loop : -3.29 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 262 TYR 0.019 0.001 TYR C 121 PHE 0.016 0.001 PHE G 307 TRP 0.011 0.001 TRP D 74 HIS 0.004 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00315 (23989) covalent geometry : angle 0.67459 (32529) SS BOND : bond 0.00150 ( 14) SS BOND : angle 0.51207 ( 28) hydrogen bonds : bond 0.07341 ( 973) hydrogen bonds : angle 4.35465 ( 2667) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 269 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7926 (mt-10) REVERT: C 351 LYS cc_start: 0.7841 (mmtm) cc_final: 0.7075 (mptt) REVERT: E 345 GLU cc_start: 0.8114 (tp30) cc_final: 0.7353 (tp30) REVERT: E 351 LYS cc_start: 0.7265 (mppt) cc_final: 0.6819 (mptt) REVERT: F 54 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.6689 (t80) REVERT: G 344 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7557 (mt-10) outliers start: 32 outliers final: 17 residues processed: 279 average time/residue: 0.1390 time to fit residues: 63.8571 Evaluate side-chains 235 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 293 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 282 optimal weight: 1.9990 chunk 247 optimal weight: 40.0000 chunk 106 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 229 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.234179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.158043 restraints weight = 28037.164| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 3.46 r_work: 0.3704 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24003 Z= 0.138 Angle : 0.627 6.137 32557 Z= 0.323 Chirality : 0.041 0.144 3766 Planarity : 0.005 0.054 4046 Dihedral : 6.299 80.584 3143 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.00 % Favored : 89.76 % Rotamer: Outliers : 1.86 % Allowed : 11.85 % Favored : 86.28 % 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 (0.16), residues: 2919 helix: 0.90 (0.15), residues: 1386 sheet: 2.12 (0.37), residues: 42 loop : -3.27 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 262 TYR 0.012 0.001 TYR A 221 PHE 0.019 0.001 PHE B 307 TRP 0.008 0.001 TRP G 74 HIS 0.002 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00299 (23989) covalent geometry : angle 0.62686 (32529) SS BOND : bond 0.00156 ( 14) SS BOND : angle 0.64104 ( 28) hydrogen bonds : bond 0.06678 ( 973) hydrogen bonds : angle 4.13958 ( 2667) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LYS cc_start: 0.7776 (mmtm) cc_final: 0.7140 (mptt) REVERT: B 344 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7472 (mt-10) REVERT: B 351 LYS cc_start: 0.7874 (mptt) cc_final: 0.7418 (mmmt) REVERT: C 351 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7261 (mptt) REVERT: E 345 GLU cc_start: 0.8142 (tp30) cc_final: 0.7421 (tp30) REVERT: E 351 LYS cc_start: 0.7366 (mppt) cc_final: 0.6912 (mptt) REVERT: F 344 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7299 (tt0) REVERT: G 344 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7593 (tt0) REVERT: G 351 LYS cc_start: 0.7720 (mmtm) cc_final: 0.7226 (mmmt) outliers start: 49 outliers final: 37 residues processed: 251 average time/residue: 0.1456 time to fit residues: 59.0059 Evaluate side-chains 255 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 303 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 213 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 142 optimal weight: 40.0000 chunk 130 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 226 optimal weight: 20.0000 chunk 247 optimal weight: 0.0170 chunk 53 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN C 282 GLN C 403 GLN F 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.229810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.153110 restraints weight = 28225.490| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 3.40 r_work: 0.3647 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24003 Z= 0.157 Angle : 0.652 6.670 32557 Z= 0.335 Chirality : 0.042 0.146 3766 Planarity : 0.005 0.053 4046 Dihedral : 6.298 79.443 3143 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.65 % Favored : 89.11 % Rotamer: Outliers : 1.90 % Allowed : 13.98 % Favored : 84.12 % 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: -1.70 (0.16), residues: 2919 helix: 0.74 (0.15), residues: 1393 sheet: 0.71 (0.45), residues: 84 loop : -3.36 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 225 TYR 0.014 0.001 TYR A 221 PHE 0.025 0.001 PHE C 307 TRP 0.011 0.001 TRP F 104 HIS 0.002 0.001 HIS G 5 Details of bonding type rmsd covalent geometry : bond 0.00372 (23989) covalent geometry : angle 0.65205 (32529) SS BOND : bond 0.00205 ( 14) SS BOND : angle 0.76373 ( 28) hydrogen bonds : bond 0.06305 ( 973) hydrogen bonds : angle 4.10021 ( 2667) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 225 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7854 (tt0) REVERT: A 351 LYS cc_start: 0.7828 (mmtm) cc_final: 0.7143 (mptt) REVERT: C 351 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7469 (mptt) REVERT: F 344 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7259 (tt0) REVERT: G 344 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7589 (tt0) REVERT: G 351 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7114 (mptt) outliers start: 50 outliers final: 38 residues processed: 250 average time/residue: 0.1566 time to fit residues: 63.1090 Evaluate side-chains 247 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 303 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 216 optimal weight: 0.0970 chunk 43 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 282 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 275 optimal weight: 3.9990 chunk 60 optimal weight: 0.0970 overall best weight: 2.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 GLN D 282 GLN F 282 GLN G 282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.228582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.152190 restraints weight = 28156.430| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.35 r_work: 0.3640 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24003 Z= 0.144 Angle : 0.640 7.393 32557 Z= 0.326 Chirality : 0.041 0.140 3766 Planarity : 0.005 0.053 4046 Dihedral : 6.226 77.616 3143 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.79 % Favored : 88.97 % Rotamer: Outliers : 2.36 % Allowed : 15.39 % Favored : 82.26 % 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: -1.74 (0.16), residues: 2919 helix: 0.74 (0.15), residues: 1393 sheet: 0.63 (0.45), residues: 84 loop : -3.41 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 262 TYR 0.015 0.001 TYR B 221 PHE 0.020 0.001 PHE B 307 TRP 0.010 0.001 TRP G 104 HIS 0.003 0.000 HIS G 5 Details of bonding type rmsd covalent geometry : bond 0.00336 (23989) covalent geometry : angle 0.64015 (32529) SS BOND : bond 0.00183 ( 14) SS BOND : angle 0.64789 ( 28) hydrogen bonds : bond 0.05852 ( 973) hydrogen bonds : angle 3.99842 ( 2667) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 239 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7894 (tt0) REVERT: A 351 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7144 (mptt) REVERT: B 128 ARG cc_start: 0.7500 (ttp-170) cc_final: 0.7258 (ttt180) REVERT: C 351 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7327 (mptt) REVERT: E 351 LYS cc_start: 0.7744 (mmtm) cc_final: 0.7050 (mptt) REVERT: F 344 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7283 (tt0) REVERT: G 344 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: G 351 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7107 (mptt) outliers start: 62 outliers final: 47 residues processed: 268 average time/residue: 0.1499 time to fit residues: 64.9763 Evaluate side-chains 266 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 344 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 256 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN E 282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.227595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.151056 restraints weight = 28498.589| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 3.41 r_work: 0.3642 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24003 Z= 0.143 Angle : 0.658 16.444 32557 Z= 0.331 Chirality : 0.041 0.146 3766 Planarity : 0.005 0.054 4046 Dihedral : 6.171 76.057 3143 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.38 % Favored : 89.38 % Rotamer: Outliers : 2.51 % Allowed : 15.81 % Favored : 81.69 % 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: -1.74 (0.16), residues: 2919 helix: 0.73 (0.15), residues: 1393 sheet: 0.60 (0.45), residues: 84 loop : -3.41 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 262 TYR 0.014 0.001 TYR A 221 PHE 0.018 0.001 PHE D 307 TRP 0.009 0.001 TRP C 104 HIS 0.005 0.000 HIS G 5 Details of bonding type rmsd covalent geometry : bond 0.00334 (23989) covalent geometry : angle 0.65781 (32529) SS BOND : bond 0.00197 ( 14) SS BOND : angle 0.64370 ( 28) hydrogen bonds : bond 0.05695 ( 973) hydrogen bonds : angle 3.97466 ( 2667) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 241 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6163 (pp20) REVERT: A 344 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8066 (tt0) REVERT: B 128 ARG cc_start: 0.7494 (ttp-170) cc_final: 0.7261 (ttt180) REVERT: B 344 GLU cc_start: 0.7439 (tt0) cc_final: 0.7237 (mt-10) REVERT: B 351 LYS cc_start: 0.8014 (mptt) cc_final: 0.7556 (mmmt) REVERT: C 351 LYS cc_start: 0.7924 (mmtm) cc_final: 0.7175 (mptt) REVERT: E 351 LYS cc_start: 0.7732 (mmtm) cc_final: 0.6906 (mptt) REVERT: F 344 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7283 (tt0) REVERT: G 344 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: G 351 LYS cc_start: 0.7745 (mmtm) cc_final: 0.7138 (mptt) outliers start: 66 outliers final: 47 residues processed: 277 average time/residue: 0.1429 time to fit residues: 63.9093 Evaluate side-chains 269 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 344 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 170 optimal weight: 0.0570 chunk 185 optimal weight: 50.0000 chunk 288 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 25 optimal weight: 0.1980 chunk 262 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 119 optimal weight: 50.0000 chunk 217 optimal weight: 0.9990 chunk 239 optimal weight: 0.0070 chunk 274 optimal weight: 9.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 GLN F 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.231323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.156109 restraints weight = 28191.966| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.41 r_work: 0.3686 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24003 Z= 0.124 Angle : 0.647 14.150 32557 Z= 0.322 Chirality : 0.041 0.178 3766 Planarity : 0.005 0.053 4046 Dihedral : 6.013 74.649 3143 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.45 % Favored : 89.31 % Rotamer: Outliers : 1.18 % Allowed : 17.74 % Favored : 81.08 % 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: -1.64 (0.16), residues: 2919 helix: 0.80 (0.15), residues: 1400 sheet: 0.39 (0.44), residues: 84 loop : -3.34 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 262 TYR 0.011 0.001 TYR A 221 PHE 0.012 0.001 PHE E 307 TRP 0.007 0.001 TRP G 74 HIS 0.004 0.000 HIS G 5 Details of bonding type rmsd covalent geometry : bond 0.00267 (23989) covalent geometry : angle 0.64744 (32529) SS BOND : bond 0.00091 ( 14) SS BOND : angle 0.42533 ( 28) hydrogen bonds : bond 0.04792 ( 973) hydrogen bonds : angle 3.82384 ( 2667) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LYS cc_start: 0.7782 (mmtm) cc_final: 0.7130 (mptt) REVERT: B 128 ARG cc_start: 0.7388 (ttp-170) cc_final: 0.7156 (ttt180) REVERT: B 351 LYS cc_start: 0.7768 (mptt) cc_final: 0.7362 (mmmt) REVERT: C 351 LYS cc_start: 0.7859 (mmtm) cc_final: 0.7112 (mptt) REVERT: E 349 GLU cc_start: 0.8009 (pm20) cc_final: 0.7752 (pm20) REVERT: E 351 LYS cc_start: 0.7679 (mmtm) cc_final: 0.6885 (mptt) REVERT: F 318 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5622 (pp20) REVERT: F 344 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7263 (tt0) REVERT: G 351 LYS cc_start: 0.7621 (mmtm) cc_final: 0.7167 (mmmt) outliers start: 31 outliers final: 21 residues processed: 254 average time/residue: 0.1447 time to fit residues: 58.9815 Evaluate side-chains 249 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 222 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 241 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 231 optimal weight: 1.9990 chunk 251 optimal weight: 50.0000 chunk 260 optimal weight: 0.0070 chunk 223 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 279 optimal weight: 4.9990 chunk 43 optimal weight: 0.0470 chunk 163 optimal weight: 0.0000 overall best weight: 0.2298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN E 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.233618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.158672 restraints weight = 27995.854| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 3.44 r_work: 0.3724 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24003 Z= 0.123 Angle : 0.645 11.785 32557 Z= 0.322 Chirality : 0.040 0.179 3766 Planarity : 0.005 0.063 4046 Dihedral : 5.895 72.805 3143 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.56 % Favored : 90.20 % Rotamer: Outliers : 0.99 % Allowed : 18.39 % Favored : 80.62 % 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: -1.53 (0.16), residues: 2919 helix: 0.92 (0.15), residues: 1400 sheet: 2.36 (0.36), residues: 42 loop : -3.28 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 262 TYR 0.011 0.001 TYR A 221 PHE 0.016 0.001 PHE A 307 TRP 0.005 0.001 TRP B 74 HIS 0.003 0.000 HIS E 5 Details of bonding type rmsd covalent geometry : bond 0.00263 (23989) covalent geometry : angle 0.64556 (32529) SS BOND : bond 0.00073 ( 14) SS BOND : angle 0.37640 ( 28) hydrogen bonds : bond 0.04377 ( 973) hydrogen bonds : angle 3.77974 ( 2667) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5777 (pp20) REVERT: B 128 ARG cc_start: 0.7325 (ttp-170) cc_final: 0.7110 (ttt180) REVERT: B 318 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5745 (pp20) REVERT: B 351 LYS cc_start: 0.7651 (mptt) cc_final: 0.7231 (mmmt) REVERT: C 351 LYS cc_start: 0.7710 (mmtm) cc_final: 0.7308 (mmmt) REVERT: D 351 LYS cc_start: 0.7373 (mmmt) cc_final: 0.6937 (mmtm) REVERT: E 349 GLU cc_start: 0.7899 (pm20) cc_final: 0.7660 (pm20) REVERT: E 399 GLU cc_start: 0.3248 (OUTLIER) cc_final: 0.2813 (mm-30) REVERT: F 318 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5777 (pp20) REVERT: G 351 LYS cc_start: 0.7454 (mmtm) cc_final: 0.7019 (mmmt) outliers start: 26 outliers final: 18 residues processed: 256 average time/residue: 0.1475 time to fit residues: 61.0065 Evaluate side-chains 250 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 222 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 89 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 167 optimal weight: 40.0000 chunk 255 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 280 optimal weight: 1.9990 chunk 86 optimal weight: 0.0270 chunk 132 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.230814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.155609 restraints weight = 28378.123| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 3.42 r_work: 0.3687 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24003 Z= 0.129 Angle : 0.655 11.679 32557 Z= 0.326 Chirality : 0.041 0.159 3766 Planarity : 0.005 0.053 4046 Dihedral : 5.834 71.153 3143 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.07 % Favored : 89.69 % Rotamer: Outliers : 0.99 % Allowed : 18.54 % Favored : 80.47 % 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: -1.54 (0.16), residues: 2919 helix: 0.94 (0.15), residues: 1393 sheet: 0.31 (0.44), residues: 84 loop : -3.32 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 TYR 0.011 0.001 TYR A 221 PHE 0.018 0.001 PHE F 307 TRP 0.007 0.001 TRP C 104 HIS 0.003 0.000 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00297 (23989) covalent geometry : angle 0.65546 (32529) SS BOND : bond 0.00170 ( 14) SS BOND : angle 0.53586 ( 28) hydrogen bonds : bond 0.04690 ( 973) hydrogen bonds : angle 3.80631 ( 2667) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5857 (pp20) REVERT: B 128 ARG cc_start: 0.7308 (ttp-170) cc_final: 0.7096 (ttt180) REVERT: B 318 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5751 (pp20) REVERT: B 351 LYS cc_start: 0.7769 (mptt) cc_final: 0.7334 (mmmt) REVERT: B 372 MET cc_start: 0.5824 (ppp) cc_final: 0.5505 (ppp) REVERT: C 318 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6132 (pp20) REVERT: C 351 LYS cc_start: 0.7800 (mmtm) cc_final: 0.7390 (mmmt) REVERT: D 318 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6019 (pp20) REVERT: D 351 LYS cc_start: 0.7401 (mmmt) cc_final: 0.6980 (mmtm) REVERT: E 349 GLU cc_start: 0.7940 (pm20) cc_final: 0.7656 (pm20) REVERT: E 351 LYS cc_start: 0.7642 (mmtm) cc_final: 0.7085 (mptt) REVERT: F 318 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5600 (pp20) REVERT: G 318 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.5958 (pp20) REVERT: G 351 LYS cc_start: 0.7474 (mmtm) cc_final: 0.7071 (mmmt) outliers start: 26 outliers final: 18 residues processed: 253 average time/residue: 0.1417 time to fit residues: 57.8933 Evaluate side-chains 247 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 318 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 50.0000 chunk 214 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 73 optimal weight: 0.0870 chunk 187 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 274 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.225886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.149340 restraints weight = 28617.137| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.41 r_work: 0.3614 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24003 Z= 0.164 Angle : 0.705 11.567 32557 Z= 0.355 Chirality : 0.043 0.173 3766 Planarity : 0.005 0.053 4046 Dihedral : 5.927 68.069 3143 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.96 % Favored : 88.80 % Rotamer: Outliers : 1.10 % Allowed : 18.39 % Favored : 80.51 % 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: -1.73 (0.16), residues: 2919 helix: 0.73 (0.15), residues: 1393 sheet: 0.54 (0.45), residues: 84 loop : -3.39 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 225 TYR 0.015 0.001 TYR A 221 PHE 0.027 0.002 PHE F 307 TRP 0.013 0.001 TRP C 104 HIS 0.005 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00393 (23989) covalent geometry : angle 0.70449 (32529) SS BOND : bond 0.00292 ( 14) SS BOND : angle 0.76563 ( 28) hydrogen bonds : bond 0.05909 ( 973) hydrogen bonds : angle 4.02652 ( 2667) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6035 (pp20) REVERT: A 351 LYS cc_start: 0.7853 (mmtm) cc_final: 0.7177 (mptt) REVERT: B 128 ARG cc_start: 0.7468 (ttp-170) cc_final: 0.7246 (ttt180) REVERT: B 318 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.5938 (pp20) REVERT: B 351 LYS cc_start: 0.7939 (mptt) cc_final: 0.7504 (mmmt) REVERT: B 372 MET cc_start: 0.5788 (ppp) cc_final: 0.5517 (ppp) REVERT: C 318 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6255 (pp20) REVERT: C 351 LYS cc_start: 0.7954 (mmtm) cc_final: 0.7302 (mptt) REVERT: D 128 ARG cc_start: 0.7700 (tmm-80) cc_final: 0.7451 (ttt180) REVERT: D 318 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6205 (pp20) REVERT: D 351 LYS cc_start: 0.7650 (mmmt) cc_final: 0.7212 (mmtm) REVERT: D 392 MET cc_start: 0.4308 (pmm) cc_final: 0.3922 (tmm) REVERT: E 318 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5927 (pp20) REVERT: E 349 GLU cc_start: 0.8127 (pm20) cc_final: 0.7845 (pm20) REVERT: E 351 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7225 (mptt) REVERT: F 318 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5760 (pp20) REVERT: G 318 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6130 (pp20) REVERT: G 351 LYS cc_start: 0.7777 (mmtm) cc_final: 0.7151 (mptt) outliers start: 29 outliers final: 19 residues processed: 229 average time/residue: 0.1550 time to fit residues: 56.5062 Evaluate side-chains 228 residues out of total 2639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 318 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 152 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 chunk 114 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 230 optimal weight: 7.9990 chunk 255 optimal weight: 0.9990 chunk 227 optimal weight: 50.0000 chunk 40 optimal weight: 50.0000 chunk 130 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.226405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.150656 restraints weight = 28384.157| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.38 r_work: 0.3626 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24003 Z= 0.143 Angle : 0.680 11.641 32557 Z= 0.342 Chirality : 0.041 0.167 3766 Planarity : 0.005 0.053 4046 Dihedral : 5.860 65.342 3143 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.89 % Favored : 88.87 % Rotamer: Outliers : 1.41 % Allowed : 18.31 % Favored : 80.28 % 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 (0.16), residues: 2919 helix: 0.77 (0.15), residues: 1393 sheet: 0.47 (0.45), residues: 84 loop : -3.41 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 262 TYR 0.014 0.001 TYR F 221 PHE 0.019 0.001 PHE A 307 TRP 0.011 0.001 TRP C 104 HIS 0.005 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00338 (23989) covalent geometry : angle 0.68008 (32529) SS BOND : bond 0.00207 ( 14) SS BOND : angle 0.62130 ( 28) hydrogen bonds : bond 0.05380 ( 973) hydrogen bonds : angle 3.94642 ( 2667) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6440.43 seconds wall clock time: 111 minutes 1.60 seconds (6661.60 seconds total)