Starting phenix.real_space_refine on Sat Aug 8 07:46:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21ro_67946/08_2026/21ro_67946.cif Found real_map, /net/cci-nas-00/data/ceres_data/21ro_67946/08_2026/21ro_67946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21ro_67946/08_2026/21ro_67946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21ro_67946/08_2026/21ro_67946.map" model { file = "/net/cci-nas-00/data/ceres_data/21ro_67946/08_2026/21ro_67946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21ro_67946/08_2026/21ro_67946.cif" } resolution = 2.68 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= -0.000 sd= 0.052 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: 6 Type Number sf(0) Gaussians P 66 5.49 5 Mg 6 5.21 5 S 138 5.16 5 C 16524 2.51 5 N 4428 2.21 5 O 5076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26238 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4173 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 491} Chain: "G" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'T8T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, F, H, I, J, K, L Time building chain proxies: 4.40, per 1000 atoms: 0.17 Number of scatterers: 26238 At special positions: 0 Unit cell: (150.36, 136.92, 106.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 138 16.00 P 66 15.00 Mg 6 11.99 O 5076 8.00 N 4428 7.00 C 16524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.65 Conformation dependent library (CDL) restraints added in 790.2 milliseconds 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 12 sheets defined 60.2% alpha, 4.9% beta 0 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.590A pdb=" N LYS A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 removed outlier: 4.052A pdb=" N ARG A 100 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE A 101 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 168 through 179 removed outlier: 3.938A pdb=" N ASN A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 198 Processing helix chain 'A' and resid 210 through 231 removed outlier: 3.734A pdb=" N SER A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 266 removed outlier: 3.675A pdb=" N LYS A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.648A pdb=" N SER A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 333 through 343 removed outlier: 3.539A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 365 removed outlier: 3.683A pdb=" N HIS A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 375 Proline residue: A 370 - end of helix removed outlier: 3.522A pdb=" N GLY A 373 " --> pdb=" O PRO A 370 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 375 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 401 Processing helix chain 'A' and resid 403 through 417 Processing helix chain 'A' and resid 422 through 433 Processing helix chain 'A' and resid 434 through 443 Processing helix chain 'A' and resid 447 through 461 removed outlier: 3.669A pdb=" N LEU A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 490 through 498 removed outlier: 3.575A pdb=" N TYR A 498 " --> pdb=" O ILE A 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 81 through 95 removed outlier: 3.590A pdb=" N LYS B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 105 removed outlier: 4.052A pdb=" N ARG B 100 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE B 101 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 140 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 168 Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.938A pdb=" N ASN B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 198 Processing helix chain 'B' and resid 210 through 231 removed outlier: 3.733A pdb=" N SER B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP B 231 " --> pdb=" O ARG B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 266 removed outlier: 3.674A pdb=" N LYS B 265 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.648A pdb=" N SER B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.539A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 365 removed outlier: 3.683A pdb=" N HIS B 364 " --> pdb=" O ASN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 375 Proline residue: B 370 - end of helix removed outlier: 3.522A pdb=" N GLY B 373 " --> pdb=" O PRO B 370 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 375 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 401 Processing helix chain 'B' and resid 403 through 417 Processing helix chain 'B' and resid 422 through 433 Processing helix chain 'B' and resid 434 through 443 Processing helix chain 'B' and resid 447 through 461 removed outlier: 3.670A pdb=" N LEU B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 490 through 498 removed outlier: 3.575A pdb=" N TYR B 498 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 17 Processing helix chain 'C' and resid 40 through 50 Processing helix chain 'C' and resid 81 through 95 removed outlier: 3.590A pdb=" N LYS C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 removed outlier: 4.053A pdb=" N ARG C 100 " --> pdb=" O GLU C 97 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 140 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 161 through 168 Processing helix chain 'C' and resid 168 through 179 removed outlier: 3.938A pdb=" N ASN C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 198 Processing helix chain 'C' and resid 210 through 231 removed outlier: 3.733A pdb=" N SER C 214 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA C 223 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP C 231 " --> pdb=" O ARG C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 266 removed outlier: 3.674A pdb=" N LYS C 265 " --> pdb=" O MET C 261 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.647A pdb=" N SER C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 311 through 329 Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.539A pdb=" N VAL C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 365 removed outlier: 3.683A pdb=" N HIS C 364 " --> pdb=" O ASN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 375 Proline residue: C 370 - end of helix removed outlier: 3.522A pdb=" N GLY C 373 " --> pdb=" O PRO C 370 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 375 " --> pdb=" O LEU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 401 Processing helix chain 'C' and resid 403 through 417 Processing helix chain 'C' and resid 422 through 433 Processing helix chain 'C' and resid 434 through 443 Processing helix chain 'C' and resid 447 through 461 removed outlier: 3.670A pdb=" N LEU C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 469 Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 490 through 498 removed outlier: 3.575A pdb=" N TYR C 498 " --> pdb=" O ILE C 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 17 Processing helix chain 'D' and resid 40 through 50 Processing helix chain 'D' and resid 81 through 95 removed outlier: 3.590A pdb=" N LYS D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 removed outlier: 4.051A pdb=" N ARG D 100 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE D 101 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 140 Processing helix chain 'D' and resid 158 through 160 No H-bonds generated for 'chain 'D' and resid 158 through 160' Processing helix chain 'D' and resid 161 through 168 Processing helix chain 'D' and resid 168 through 179 removed outlier: 3.937A pdb=" N ASN D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 198 Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.733A pdb=" N SER D 214 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL D 224 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 266 removed outlier: 3.675A pdb=" N LYS D 265 " --> pdb=" O MET D 261 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.649A pdb=" N SER D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 309 Processing helix chain 'D' and resid 311 through 329 Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.539A pdb=" N VAL D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 365 removed outlier: 3.682A pdb=" N HIS D 364 " --> pdb=" O ASN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 375 Proline residue: D 370 - end of helix removed outlier: 3.522A pdb=" N GLY D 373 " --> pdb=" O PRO D 370 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 375 " --> pdb=" O LEU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 401 Processing helix chain 'D' and resid 403 through 417 Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 434 through 443 Processing helix chain 'D' and resid 447 through 461 removed outlier: 3.669A pdb=" N LEU D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 469 Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 490 through 498 removed outlier: 3.575A pdb=" N TYR D 498 " --> pdb=" O ILE D 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 17 Processing helix chain 'E' and resid 40 through 50 Processing helix chain 'E' and resid 81 through 95 removed outlier: 3.589A pdb=" N LYS E 87 " --> pdb=" O LYS E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 105 removed outlier: 4.052A pdb=" N ARG E 100 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE E 101 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 140 Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 161 through 168 Processing helix chain 'E' and resid 168 through 179 removed outlier: 3.937A pdb=" N ASN E 177 " --> pdb=" O LYS E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 198 Processing helix chain 'E' and resid 210 through 231 removed outlier: 3.734A pdb=" N SER E 214 " --> pdb=" O PRO E 210 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA E 223 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 266 removed outlier: 3.674A pdb=" N LYS E 265 " --> pdb=" O MET E 261 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 295 removed outlier: 3.648A pdb=" N SER E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 309 Processing helix chain 'E' and resid 311 through 329 Processing helix chain 'E' and resid 333 through 343 removed outlier: 3.539A pdb=" N VAL E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 365 removed outlier: 3.683A pdb=" N HIS E 364 " --> pdb=" O ASN E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 375 Proline residue: E 370 - end of helix removed outlier: 3.523A pdb=" N GLY E 373 " --> pdb=" O PRO E 370 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU E 375 " --> pdb=" O LEU E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 401 Processing helix chain 'E' and resid 403 through 417 Processing helix chain 'E' and resid 422 through 433 Processing helix chain 'E' and resid 434 through 443 Processing helix chain 'E' and resid 447 through 461 removed outlier: 3.669A pdb=" N LEU E 461 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 469 Processing helix chain 'E' and resid 470 through 480 Processing helix chain 'E' and resid 490 through 498 removed outlier: 3.575A pdb=" N TYR E 498 " --> pdb=" O ILE E 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 17 Processing helix chain 'F' and resid 40 through 50 Processing helix chain 'F' and resid 81 through 95 removed outlier: 3.590A pdb=" N LYS F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 removed outlier: 4.053A pdb=" N ARG F 100 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE F 101 " --> pdb=" O GLU F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 140 Processing helix chain 'F' and resid 158 through 160 No H-bonds generated for 'chain 'F' and resid 158 through 160' Processing helix chain 'F' and resid 161 through 168 Processing helix chain 'F' and resid 168 through 179 removed outlier: 3.938A pdb=" N ASN F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 198 Processing helix chain 'F' and resid 210 through 231 removed outlier: 3.733A pdb=" N SER F 214 " --> pdb=" O PRO F 210 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL F 224 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 266 removed outlier: 3.673A pdb=" N LYS F 265 " --> pdb=" O MET F 261 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR F 266 " --> pdb=" O GLU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 295 removed outlier: 3.648A pdb=" N SER F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 309 Processing helix chain 'F' and resid 311 through 329 Processing helix chain 'F' and resid 333 through 343 removed outlier: 3.539A pdb=" N VAL F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 365 removed outlier: 3.683A pdb=" N HIS F 364 " --> pdb=" O ASN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 375 Proline residue: F 370 - end of helix removed outlier: 3.523A pdb=" N GLY F 373 " --> pdb=" O PRO F 370 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU F 375 " --> pdb=" O LEU F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 401 Processing helix chain 'F' and resid 403 through 417 Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 434 through 443 Processing helix chain 'F' and resid 447 through 461 removed outlier: 3.670A pdb=" N LEU F 461 " --> pdb=" O ASP F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 469 Processing helix chain 'F' and resid 470 through 480 Processing helix chain 'F' and resid 490 through 498 removed outlier: 3.575A pdb=" N TYR F 498 " --> pdb=" O ILE F 494 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 235 through 237 Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 Processing sheet with id=AA4, first strand: chain 'B' and resid 235 through 237 Processing sheet with id=AA5, first strand: chain 'C' and resid 63 through 68 Processing sheet with id=AA6, first strand: chain 'C' and resid 235 through 237 Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 68 Processing sheet with id=AA8, first strand: chain 'D' and resid 235 through 237 Processing sheet with id=AA9, first strand: chain 'E' and resid 63 through 68 Processing sheet with id=AB1, first strand: chain 'E' and resid 235 through 237 Processing sheet with id=AB2, first strand: chain 'F' and resid 63 through 68 Processing sheet with id=AB3, first strand: chain 'F' and resid 235 through 237 1243 hydrogen bonds defined for protein. 3513 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 11328 1.40 - 1.57: 15348 1.57 - 1.74: 108 1.74 - 1.91: 186 1.91 - 2.08: 6 Bond restraints: 26976 Sorted by residual: bond pdb=" O3B T8T B 601 " pdb=" PG T8T B 601 " ideal model delta sigma weight residual 1.778 1.610 0.168 2.00e-02 2.50e+03 7.02e+01 bond pdb=" O3B T8T C 601 " pdb=" PG T8T C 601 " ideal model delta sigma weight residual 1.778 1.611 0.167 2.00e-02 2.50e+03 7.01e+01 bond pdb=" O3B T8T F 601 " pdb=" PG T8T F 601 " ideal model delta sigma weight residual 1.778 1.611 0.167 2.00e-02 2.50e+03 7.01e+01 bond pdb=" O3B T8T A 601 " pdb=" PG T8T A 601 " ideal model delta sigma weight residual 1.778 1.611 0.167 2.00e-02 2.50e+03 7.01e+01 bond pdb=" O3B T8T E 601 " pdb=" PG T8T E 601 " ideal model delta sigma weight residual 1.778 1.611 0.167 2.00e-02 2.50e+03 6.99e+01 ... (remaining 26971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 36482 2.16 - 4.32: 202 4.32 - 6.48: 66 6.48 - 8.64: 0 8.64 - 10.81: 6 Bond angle restraints: 36756 Sorted by residual: angle pdb=" O4' DA I 6 " pdb=" C4' DA I 6 " pdb=" C3' DA I 6 " ideal model delta sigma weight residual 106.00 103.52 2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" O4' DA L 6 " pdb=" C4' DA L 6 " pdb=" C3' DA L 6 " ideal model delta sigma weight residual 106.00 103.52 2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" O4' DA J 6 " pdb=" C4' DA J 6 " pdb=" C3' DA J 6 " ideal model delta sigma weight residual 106.00 103.53 2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" O4' DA H 6 " pdb=" C4' DA H 6 " pdb=" C3' DA H 6 " ideal model delta sigma weight residual 106.00 103.56 2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" O4' DA G 6 " pdb=" C4' DA G 6 " pdb=" C3' DA G 6 " ideal model delta sigma weight residual 106.00 103.57 2.43 6.00e-01 2.78e+00 1.64e+01 ... (remaining 36751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13410 17.93 - 35.86: 1944 35.86 - 53.79: 666 53.79 - 71.72: 162 71.72 - 89.65: 60 Dihedral angle restraints: 16242 sinusoidal: 7158 harmonic: 9084 Sorted by residual: dihedral pdb=" CB GLU F 98 " pdb=" CG GLU F 98 " pdb=" CD GLU F 98 " pdb=" OE1 GLU F 98 " ideal model delta sinusoidal sigma weight residual 0.00 89.65 -89.65 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 98 " pdb=" CG GLU A 98 " pdb=" CD GLU A 98 " pdb=" OE1 GLU A 98 " ideal model delta sinusoidal sigma weight residual 0.00 89.64 -89.64 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 98 " pdb=" CG GLU B 98 " pdb=" CD GLU B 98 " pdb=" OE1 GLU B 98 " ideal model delta sinusoidal sigma weight residual 0.00 89.63 -89.63 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 16239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2360 0.025 - 0.050: 968 0.050 - 0.075: 391 0.075 - 0.100: 135 0.100 - 0.125: 94 Chirality restraints: 3948 Sorted by residual: chirality pdb=" C1' T8T D 601 " pdb=" C2' T8T D 601 " pdb=" N9 T8T D 601 " pdb=" O4' T8T D 601 " both_signs ideal model delta sigma weight residual False 2.30 2.42 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" C1' T8T A 601 " pdb=" C2' T8T A 601 " pdb=" N9 T8T A 601 " pdb=" O4' T8T A 601 " both_signs ideal model delta sigma weight residual False 2.30 2.42 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 3945 not shown) Planarity restraints: 4518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 209 " 0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO F 210 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 210 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 210 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 209 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO B 210 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 209 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO C 210 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 210 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 210 " -0.023 5.00e-02 4.00e+02 ... (remaining 4515 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 12 2.03 - 2.75: 2365 2.75 - 3.46: 35872 3.46 - 4.18: 62253 4.18 - 4.90: 114954 Nonbonded interactions: 215456 Sorted by model distance: nonbonded pdb=" OH TYR A 125 " pdb=" OP1 DA G 1 " model vdw 1.312 3.040 nonbonded pdb=" OH TYR F 125 " pdb=" OP1 DA K 1 " model vdw 1.351 3.040 nonbonded pdb=" OH TYR F 125 " pdb=" P DA K 1 " model vdw 1.485 3.400 nonbonded pdb=" OH TYR C 125 " pdb=" P DA H 1 " model vdw 1.522 3.400 nonbonded pdb=" OH TYR C 125 " pdb=" OP1 DA H 1 " model vdw 1.529 3.040 ... (remaining 215451 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.690 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:8.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 0.004 0.168 26976 Z= 0.254 Angle : 0.467 10.806 36756 Z= 0.250 Chirality : 0.037 0.125 3948 Planarity : 0.003 0.042 4518 Dihedral : 19.504 89.655 10398 Min Nonbonded Distance : 1.312 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.64 % Allowed : 22.75 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.73 (0.15), residues: 3042 helix: 1.33 (0.12), residues: 1728 sheet: -0.75 (0.34), residues: 228 loop : -0.53 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 301 TYR 0.009 0.001 TYR F 238 PHE 0.006 0.001 PHE A 454 TRP 0.009 0.001 TRP E 288 HIS 0.001 0.000 HIS F 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.25 (26976) covalent geometry : angle 0.46704 / 0.25 (36756) hydrogen bonds : bond 0.14624 / 9.71 ( 1243) hydrogen bonds : angle 5.42968 / 4.04 ( 3513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 1.005 Fit side-chains REVERT: A 11 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7923 (t80) REVERT: A 227 ARG cc_start: 0.8238 (tpt-90) cc_final: 0.7295 (tpp-160) REVERT: A 287 ASN cc_start: 0.7980 (p0) cc_final: 0.7718 (p0) REVERT: A 333 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8404 (m) REVERT: A 348 GLU cc_start: 0.7385 (mp0) cc_final: 0.6594 (tp30) REVERT: A 462 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7241 (t0) REVERT: A 490 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7396 (mmtt) REVERT: B 11 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7048 (t80) REVERT: B 109 MET cc_start: 0.8663 (mmp) cc_final: 0.8451 (mmp) REVERT: B 227 ARG cc_start: 0.8273 (tpt-90) cc_final: 0.7374 (tpp-160) REVERT: B 287 ASN cc_start: 0.7953 (p0) cc_final: 0.7741 (p0) REVERT: B 348 GLU cc_start: 0.7175 (mp0) cc_final: 0.6521 (tt0) REVERT: B 462 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7279 (t0) REVERT: B 490 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7456 (mmtt) REVERT: C 227 ARG cc_start: 0.8199 (tpt-90) cc_final: 0.7251 (tpp-160) REVERT: C 348 GLU cc_start: 0.7148 (mp0) cc_final: 0.6368 (tp30) REVERT: C 397 MET cc_start: 0.8066 (tmt) cc_final: 0.7837 (tmt) REVERT: C 462 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7180 (t0) REVERT: C 490 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7461 (mmtt) REVERT: D 11 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7913 (t80) REVERT: D 227 ARG cc_start: 0.8243 (tpt-90) cc_final: 0.7294 (tpp-160) REVERT: D 287 ASN cc_start: 0.7996 (p0) cc_final: 0.7760 (p0) REVERT: D 333 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8374 (m) REVERT: D 348 GLU cc_start: 0.7379 (mp0) cc_final: 0.6577 (tp30) REVERT: D 462 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7229 (t0) REVERT: D 490 LYS cc_start: 0.8056 (mmtm) cc_final: 0.7386 (mmtt) REVERT: E 11 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7046 (t80) REVERT: E 109 MET cc_start: 0.8646 (mmp) cc_final: 0.8445 (mmp) REVERT: E 227 ARG cc_start: 0.8292 (tpt-90) cc_final: 0.7394 (tpp-160) REVERT: E 287 ASN cc_start: 0.7968 (p0) cc_final: 0.7763 (p0) REVERT: E 348 GLU cc_start: 0.7160 (mp0) cc_final: 0.6512 (tt0) REVERT: E 462 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7268 (t0) REVERT: E 490 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7470 (mmtt) REVERT: F 227 ARG cc_start: 0.8192 (tpt-90) cc_final: 0.7276 (tpp-160) REVERT: F 348 GLU cc_start: 0.7144 (mp0) cc_final: 0.6369 (tp30) REVERT: F 397 MET cc_start: 0.8074 (tmt) cc_final: 0.7834 (tmt) REVERT: F 462 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7168 (t0) REVERT: F 490 LYS cc_start: 0.8057 (mmtm) cc_final: 0.7452 (mmtt) outliers start: 18 outliers final: 6 residues processed: 217 average time/residue: 0.5570 time to fit residues: 143.5862 Evaluate side-chains 204 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 462 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.0170 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN B 324 GLN C 324 GLN D 324 GLN E 324 GLN F 324 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.160426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132279 restraints weight = 28942.803| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.91 r_work: 0.3408 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26976 Z= 0.101 Angle : 0.386 4.871 36756 Z= 0.220 Chirality : 0.037 0.126 3948 Planarity : 0.004 0.044 4518 Dihedral : 14.902 98.619 4272 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.18 % Allowed : 22.00 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.35 (0.15), residues: 3042 helix: 1.93 (0.13), residues: 1734 sheet: -0.49 (0.33), residues: 228 loop : -0.47 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 119 TYR 0.011 0.001 TYR E 238 PHE 0.014 0.001 PHE F 432 TRP 0.007 0.001 TRP B 288 HIS 0.002 0.000 HIS E 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.10 (26976) covalent geometry : angle 0.38574 / 0.22 (36756) hydrogen bonds : bond 0.03875 / 2.60 ( 1243) hydrogen bonds : angle 4.25916 / 3.11 ( 3513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 1.208 Fit side-chains REVERT: A 11 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.7899 (t80) REVERT: A 124 ASN cc_start: 0.7347 (t0) cc_final: 0.6435 (p0) REVERT: A 189 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: A 227 ARG cc_start: 0.8327 (tpt-90) cc_final: 0.7295 (tpp-160) REVERT: A 287 ASN cc_start: 0.8091 (p0) cc_final: 0.7823 (p0) REVERT: A 333 SER cc_start: 0.8809 (OUTLIER) cc_final: 0.8523 (m) REVERT: A 462 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7062 (t0) REVERT: A 490 LYS cc_start: 0.7846 (mmtm) cc_final: 0.7139 (mmtt) REVERT: B 11 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.7041 (t80) REVERT: B 124 ASN cc_start: 0.7233 (t0) cc_final: 0.6278 (p0) REVERT: B 227 ARG cc_start: 0.8343 (tpt-90) cc_final: 0.7384 (tpp-160) REVERT: B 287 ASN cc_start: 0.8094 (p0) cc_final: 0.7856 (p0) REVERT: B 348 GLU cc_start: 0.7002 (mp0) cc_final: 0.6343 (tt0) REVERT: B 490 LYS cc_start: 0.7885 (mmtm) cc_final: 0.7175 (mmtt) REVERT: C 124 ASN cc_start: 0.7387 (t0) cc_final: 0.6438 (p0) REVERT: C 227 ARG cc_start: 0.8237 (tpt-90) cc_final: 0.7231 (tpp-160) REVERT: C 348 GLU cc_start: 0.6997 (mp0) cc_final: 0.6241 (tp30) REVERT: C 397 MET cc_start: 0.7964 (tmt) cc_final: 0.7735 (tmt) REVERT: C 490 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7253 (mmtt) REVERT: D 11 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8070 (t80) REVERT: D 124 ASN cc_start: 0.7346 (t0) cc_final: 0.6371 (p0) REVERT: D 189 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: D 227 ARG cc_start: 0.8341 (tpt-90) cc_final: 0.7288 (tpp-160) REVERT: D 287 ASN cc_start: 0.8074 (p0) cc_final: 0.7810 (p0) REVERT: D 462 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7069 (t0) REVERT: D 490 LYS cc_start: 0.7871 (mmtm) cc_final: 0.7153 (mmtt) REVERT: E 11 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.7051 (t80) REVERT: E 124 ASN cc_start: 0.7268 (t0) cc_final: 0.6494 (p0) REVERT: E 227 ARG cc_start: 0.8333 (tpt-90) cc_final: 0.7380 (tpp-160) REVERT: E 287 ASN cc_start: 0.8048 (p0) cc_final: 0.7807 (p0) REVERT: E 348 GLU cc_start: 0.7044 (mp0) cc_final: 0.6379 (tt0) REVERT: E 490 LYS cc_start: 0.7884 (mmtm) cc_final: 0.7168 (mmtt) REVERT: F 124 ASN cc_start: 0.7383 (t0) cc_final: 0.6556 (p0) REVERT: F 227 ARG cc_start: 0.8237 (tpt-90) cc_final: 0.7242 (tpp-160) REVERT: F 348 GLU cc_start: 0.6990 (mp0) cc_final: 0.6226 (tp30) REVERT: F 397 MET cc_start: 0.7959 (tmt) cc_final: 0.7721 (tmt) REVERT: F 490 LYS cc_start: 0.7875 (mmtm) cc_final: 0.7207 (mmtt) outliers start: 33 outliers final: 12 residues processed: 225 average time/residue: 0.5546 time to fit residues: 147.1666 Evaluate side-chains 213 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain E residue 328 GLN Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 272 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 273 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 158 optimal weight: 8.9990 chunk 294 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 89 optimal weight: 0.3980 chunk 96 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 115 optimal weight: 0.0870 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.159151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.131006 restraints weight = 28831.915| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.90 r_work: 0.3409 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 26976 Z= 0.093 Angle : 0.371 4.804 36756 Z= 0.212 Chirality : 0.036 0.122 3948 Planarity : 0.003 0.040 4518 Dihedral : 14.439 103.052 4259 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.22 % Allowed : 20.99 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.61 (0.15), residues: 3042 helix: 2.15 (0.13), residues: 1734 sheet: -0.06 (0.33), residues: 216 loop : -0.44 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 236 TYR 0.012 0.001 TYR B 238 PHE 0.004 0.001 PHE F 432 TRP 0.007 0.001 TRP E 288 HIS 0.002 0.000 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.09 (26976) covalent geometry : angle 0.37056 / 0.21 (36756) hydrogen bonds : bond 0.03420 / 2.29 ( 1243) hydrogen bonds : angle 3.88429 / 2.81 ( 3513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 1.005 Fit side-chains REVERT: A 11 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.7918 (t80) REVERT: A 29 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: A 109 MET cc_start: 0.8512 (mmt) cc_final: 0.8184 (mmt) REVERT: A 124 ASN cc_start: 0.7405 (t0) cc_final: 0.6475 (p0) REVERT: A 227 ARG cc_start: 0.8337 (tpt-90) cc_final: 0.7296 (tpp-160) REVERT: A 287 ASN cc_start: 0.8057 (p0) cc_final: 0.7803 (p0) REVERT: A 402 LYS cc_start: 0.8545 (mmmt) cc_final: 0.7825 (mmtt) REVERT: A 490 LYS cc_start: 0.7916 (mmtm) cc_final: 0.7193 (mmtt) REVERT: B 11 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.7121 (t80) REVERT: B 106 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7256 (pm20) REVERT: B 124 ASN cc_start: 0.7242 (t0) cc_final: 0.6283 (p0) REVERT: B 227 ARG cc_start: 0.8366 (tpt-90) cc_final: 0.7420 (tpp-160) REVERT: B 402 LYS cc_start: 0.8445 (mmmt) cc_final: 0.7703 (mmtt) REVERT: B 462 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7085 (t0) REVERT: B 490 LYS cc_start: 0.7954 (mmtm) cc_final: 0.7242 (mmtt) REVERT: C 11 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.8231 (t80) REVERT: C 124 ASN cc_start: 0.7388 (t0) cc_final: 0.6450 (p0) REVERT: C 227 ARG cc_start: 0.8267 (tpt-90) cc_final: 0.7288 (tpp-160) REVERT: C 462 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.6941 (t0) REVERT: C 490 LYS cc_start: 0.7954 (mmtm) cc_final: 0.7279 (mmtt) REVERT: D 11 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.8008 (t80) REVERT: D 29 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: D 106 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7338 (pm20) REVERT: D 109 MET cc_start: 0.8481 (mmt) cc_final: 0.8161 (mmt) REVERT: D 124 ASN cc_start: 0.7370 (t0) cc_final: 0.6430 (p0) REVERT: D 227 ARG cc_start: 0.8344 (tpt-90) cc_final: 0.7298 (tpp-160) REVERT: D 287 ASN cc_start: 0.8059 (p0) cc_final: 0.7809 (p0) REVERT: D 402 LYS cc_start: 0.8590 (mmmt) cc_final: 0.7851 (mmtt) REVERT: D 490 LYS cc_start: 0.7908 (mmtm) cc_final: 0.7172 (mmtt) REVERT: E 11 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7155 (t80) REVERT: E 106 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7298 (pm20) REVERT: E 124 ASN cc_start: 0.7251 (t0) cc_final: 0.6497 (p0) REVERT: E 227 ARG cc_start: 0.8372 (tpt-90) cc_final: 0.7437 (tpp-160) REVERT: E 402 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7685 (mmtt) REVERT: E 462 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7083 (t0) REVERT: E 490 LYS cc_start: 0.7933 (mmtm) cc_final: 0.7233 (mmtt) REVERT: F 11 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.8185 (t80) REVERT: F 124 ASN cc_start: 0.7433 (t0) cc_final: 0.6563 (p0) REVERT: F 227 ARG cc_start: 0.8303 (tpt-90) cc_final: 0.7315 (tpp-160) REVERT: F 462 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.6977 (t0) REVERT: F 490 LYS cc_start: 0.7925 (mmtm) cc_final: 0.7252 (mmtt) outliers start: 62 outliers final: 16 residues processed: 266 average time/residue: 0.6338 time to fit residues: 196.9471 Evaluate side-chains 240 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 462 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 35 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 262 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 210 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.154677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126319 restraints weight = 28692.186| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.89 r_work: 0.3353 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26976 Z= 0.122 Angle : 0.425 4.816 36756 Z= 0.240 Chirality : 0.038 0.129 3948 Planarity : 0.004 0.044 4518 Dihedral : 14.394 100.016 4254 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.79 % Allowed : 20.57 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.43 (0.15), residues: 3042 helix: 2.02 (0.13), residues: 1722 sheet: -0.24 (0.32), residues: 228 loop : -0.51 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 236 TYR 0.023 0.001 TYR D 238 PHE 0.006 0.001 PHE E 318 TRP 0.010 0.001 TRP B 288 HIS 0.003 0.001 HIS A 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (26976) covalent geometry : angle 0.42488 / 0.24 (36756) hydrogen bonds : bond 0.04114 / 2.76 ( 1243) hydrogen bonds : angle 3.92752 / 2.84 ( 3513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 2.808 Fit side-chains REVERT: A 29 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: A 124 ASN cc_start: 0.7554 (t0) cc_final: 0.6619 (p0) REVERT: A 189 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: A 227 ARG cc_start: 0.8389 (tpt-90) cc_final: 0.7327 (tpp-160) REVERT: A 287 ASN cc_start: 0.8132 (p0) cc_final: 0.7879 (p0) REVERT: A 333 SER cc_start: 0.8823 (OUTLIER) cc_final: 0.8585 (m) REVERT: A 490 LYS cc_start: 0.7928 (mmtm) cc_final: 0.7192 (mmtt) REVERT: B 11 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.7148 (t80) REVERT: B 124 ASN cc_start: 0.7412 (t0) cc_final: 0.6475 (p0) REVERT: B 227 ARG cc_start: 0.8354 (tpt-90) cc_final: 0.7408 (tpp-160) REVERT: B 287 ASN cc_start: 0.8191 (p0) cc_final: 0.7959 (p0) REVERT: B 462 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7176 (t0) REVERT: B 490 LYS cc_start: 0.8014 (mmtm) cc_final: 0.7269 (mmtt) REVERT: C 11 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8056 (t80) REVERT: C 58 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: C 124 ASN cc_start: 0.7469 (t0) cc_final: 0.6622 (p0) REVERT: C 227 ARG cc_start: 0.8331 (tpt-90) cc_final: 0.7307 (tpp-160) REVERT: C 309 LYS cc_start: 0.7543 (mtmt) cc_final: 0.7250 (mmtt) REVERT: C 462 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7028 (t0) REVERT: C 490 LYS cc_start: 0.8017 (mmtm) cc_final: 0.7307 (mmtt) REVERT: D 29 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: D 124 ASN cc_start: 0.7515 (t0) cc_final: 0.6585 (p0) REVERT: D 189 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: D 227 ARG cc_start: 0.8389 (tpt-90) cc_final: 0.7342 (tpp-160) REVERT: D 287 ASN cc_start: 0.8120 (p0) cc_final: 0.7856 (p0) REVERT: D 309 LYS cc_start: 0.7594 (mtmt) cc_final: 0.7244 (mmtt) REVERT: D 490 LYS cc_start: 0.7943 (mmtm) cc_final: 0.7196 (mmtt) REVERT: E 11 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7171 (t80) REVERT: E 124 ASN cc_start: 0.7329 (t0) cc_final: 0.6512 (p0) REVERT: E 227 ARG cc_start: 0.8335 (tpt-90) cc_final: 0.7404 (tpp-160) REVERT: E 287 ASN cc_start: 0.8171 (p0) cc_final: 0.7935 (p0) REVERT: E 462 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7174 (t0) REVERT: E 490 LYS cc_start: 0.7994 (mmtm) cc_final: 0.7244 (mmtt) REVERT: F 11 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8026 (t80) REVERT: F 124 ASN cc_start: 0.7501 (t0) cc_final: 0.6735 (p0) REVERT: F 227 ARG cc_start: 0.8380 (tpt-90) cc_final: 0.7363 (tpp-160) REVERT: F 462 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7021 (t0) REVERT: F 490 LYS cc_start: 0.7998 (mmtm) cc_final: 0.7289 (mmtt) outliers start: 50 outliers final: 14 residues processed: 235 average time/residue: 0.6537 time to fit residues: 179.4109 Evaluate side-chains 220 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 328 GLN Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 462 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 53 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 HIS A 197 GLN C 9 HIS C 197 GLN D 9 HIS D 197 GLN F 9 HIS F 197 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.150250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.122005 restraints weight = 28886.821| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.87 r_work: 0.3276 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 26976 Z= 0.195 Angle : 0.516 4.986 36756 Z= 0.286 Chirality : 0.042 0.141 3948 Planarity : 0.005 0.042 4518 Dihedral : 14.536 94.963 4250 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.61 % Allowed : 19.71 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.09 (0.15), residues: 3042 helix: 1.68 (0.12), residues: 1704 sheet: -0.24 (0.31), residues: 228 loop : -0.53 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 236 TYR 0.034 0.002 TYR A 238 PHE 0.008 0.002 PHE F 432 TRP 0.012 0.002 TRP E 288 HIS 0.003 0.001 HIS C 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 (26976) covalent geometry : angle 0.51578 / 0.29 (36756) hydrogen bonds : bond 0.05257 / 3.53 ( 1243) hydrogen bonds : angle 4.14464 / 3.01 ( 3513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 186 time to evaluate : 1.055 Fit side-chains REVERT: A 124 ASN cc_start: 0.7785 (t0) cc_final: 0.6841 (p0) REVERT: A 189 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: A 227 ARG cc_start: 0.8418 (tpt-90) cc_final: 0.7370 (tpp-160) REVERT: A 287 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7925 (p0) REVERT: A 333 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8617 (m) REVERT: A 462 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7078 (t0) REVERT: A 490 LYS cc_start: 0.7931 (mmtm) cc_final: 0.7196 (mmtt) REVERT: B 11 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.7086 (t80) REVERT: B 124 ASN cc_start: 0.7449 (t0) cc_final: 0.6580 (p0) REVERT: B 227 ARG cc_start: 0.8381 (tpt-90) cc_final: 0.7396 (tpp-160) REVERT: B 287 ASN cc_start: 0.8270 (p0) cc_final: 0.8050 (p0) REVERT: B 462 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7276 (t0) REVERT: B 490 LYS cc_start: 0.8059 (mmtm) cc_final: 0.7223 (mmtt) REVERT: C 11 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8276 (t80) REVERT: C 58 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: C 124 ASN cc_start: 0.7454 (t0) cc_final: 0.6655 (p0) REVERT: C 227 ARG cc_start: 0.8359 (tpt-90) cc_final: 0.7327 (tpp-160) REVERT: C 462 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7104 (t0) REVERT: C 490 LYS cc_start: 0.8027 (mmtm) cc_final: 0.7335 (mmmt) REVERT: D 124 ASN cc_start: 0.7638 (t0) cc_final: 0.6705 (p0) REVERT: D 189 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: D 227 ARG cc_start: 0.8419 (tpt-90) cc_final: 0.7385 (tpp-160) REVERT: D 287 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7937 (p0) REVERT: D 462 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7102 (t0) REVERT: D 490 LYS cc_start: 0.7923 (mmtm) cc_final: 0.7165 (mmtt) REVERT: E 11 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.7070 (t80) REVERT: E 124 ASN cc_start: 0.7465 (t0) cc_final: 0.6613 (p0) REVERT: E 227 ARG cc_start: 0.8370 (tpt-90) cc_final: 0.7396 (tpp-160) REVERT: E 287 ASN cc_start: 0.8270 (p0) cc_final: 0.8045 (p0) REVERT: E 462 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7277 (t0) REVERT: E 490 LYS cc_start: 0.8067 (mmtm) cc_final: 0.7230 (mmtt) REVERT: F 11 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8279 (t80) REVERT: F 58 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: F 124 ASN cc_start: 0.7610 (t0) cc_final: 0.6821 (p0) REVERT: F 227 ARG cc_start: 0.8403 (tpt-90) cc_final: 0.7351 (tpp-160) REVERT: F 462 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7092 (t0) REVERT: F 490 LYS cc_start: 0.8037 (mmtm) cc_final: 0.7345 (mmmt) outliers start: 73 outliers final: 22 residues processed: 237 average time/residue: 0.5803 time to fit residues: 162.9166 Evaluate side-chains 220 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 328 GLN Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 462 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 17 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 253 optimal weight: 3.9990 chunk 248 optimal weight: 0.0170 chunk 109 optimal weight: 0.9980 chunk 268 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.153857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125628 restraints weight = 28902.115| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.89 r_work: 0.3345 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26976 Z= 0.099 Angle : 0.407 4.768 36756 Z= 0.231 Chirality : 0.037 0.124 3948 Planarity : 0.004 0.045 4518 Dihedral : 14.406 99.649 4250 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.68 % Allowed : 21.24 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.29 (0.15), residues: 3042 helix: 1.90 (0.13), residues: 1722 sheet: -0.01 (0.32), residues: 216 loop : -0.62 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 119 TYR 0.012 0.001 TYR A 238 PHE 0.005 0.001 PHE E 318 TRP 0.011 0.001 TRP B 288 HIS 0.002 0.000 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 (26976) covalent geometry : angle 0.40738 / 0.23 (36756) hydrogen bonds : bond 0.03720 / 2.50 ( 1243) hydrogen bonds : angle 3.93692 / 2.85 ( 3513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 1.063 Fit side-chains REVERT: A 124 ASN cc_start: 0.7693 (t0) cc_final: 0.6798 (p0) REVERT: A 227 ARG cc_start: 0.8406 (tpt-90) cc_final: 0.7370 (tpp-160) REVERT: A 287 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7841 (p0) REVERT: A 460 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7114 (mtpt) REVERT: A 462 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7075 (t0) REVERT: A 490 LYS cc_start: 0.7877 (mmtm) cc_final: 0.7150 (mmtt) REVERT: B 11 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.7141 (t80) REVERT: B 58 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: B 124 ASN cc_start: 0.7419 (t0) cc_final: 0.6552 (p0) REVERT: B 227 ARG cc_start: 0.8347 (tpt-90) cc_final: 0.7381 (tpp-160) REVERT: B 460 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7277 (mtpt) REVERT: B 462 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7225 (t0) REVERT: B 490 LYS cc_start: 0.8025 (mmtm) cc_final: 0.7213 (mmtt) REVERT: C 11 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7963 (t80) REVERT: C 124 ASN cc_start: 0.7583 (t0) cc_final: 0.6757 (p0) REVERT: C 227 ARG cc_start: 0.8337 (tpt-90) cc_final: 0.7338 (tpp-160) REVERT: C 462 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7019 (t0) REVERT: C 490 LYS cc_start: 0.7979 (mmtm) cc_final: 0.7235 (mmtt) REVERT: D 124 ASN cc_start: 0.7611 (t0) cc_final: 0.6699 (p0) REVERT: D 227 ARG cc_start: 0.8394 (tpt-90) cc_final: 0.7371 (tpp-160) REVERT: D 287 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7838 (p0) REVERT: D 460 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7108 (mtpt) REVERT: D 462 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7079 (t0) REVERT: D 490 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7127 (mmtt) REVERT: E 11 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.7163 (t80) REVERT: E 58 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7333 (mt0) REVERT: E 124 ASN cc_start: 0.7398 (t0) cc_final: 0.6563 (p0) REVERT: E 227 ARG cc_start: 0.8350 (tpt-90) cc_final: 0.7388 (tpp-160) REVERT: E 287 ASN cc_start: 0.8130 (p0) cc_final: 0.7906 (p0) REVERT: E 460 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7276 (mtpt) REVERT: E 462 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7229 (t0) REVERT: E 490 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7227 (mmtt) REVERT: F 11 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7976 (t80) REVERT: F 124 ASN cc_start: 0.7562 (t0) cc_final: 0.6799 (p0) REVERT: F 227 ARG cc_start: 0.8385 (tpt-90) cc_final: 0.7367 (tpp-160) REVERT: F 462 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7022 (t0) REVERT: F 490 LYS cc_start: 0.7976 (mmtm) cc_final: 0.7234 (mmtt) outliers start: 47 outliers final: 14 residues processed: 232 average time/residue: 0.6115 time to fit residues: 167.1287 Evaluate side-chains 226 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 460 LYS Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 462 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 158 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 220 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 271 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 86 optimal weight: 0.1980 chunk 234 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.153624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125378 restraints weight = 28906.762| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.89 r_work: 0.3304 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26976 Z= 0.109 Angle : 0.417 4.765 36756 Z= 0.235 Chirality : 0.038 0.122 3948 Planarity : 0.004 0.043 4518 Dihedral : 14.323 98.950 4250 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.86 % Allowed : 21.14 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.30 (0.15), residues: 3042 helix: 1.93 (0.13), residues: 1722 sheet: -0.23 (0.32), residues: 228 loop : -0.60 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 119 TYR 0.018 0.001 TYR E 238 PHE 0.005 0.001 PHE E 318 TRP 0.010 0.001 TRP B 288 HIS 0.002 0.000 HIS D 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (26976) covalent geometry : angle 0.41678 / 0.24 (36756) hydrogen bonds : bond 0.03824 / 2.56 ( 1243) hydrogen bonds : angle 3.88941 / 2.81 ( 3513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 194 time to evaluate : 1.028 Fit side-chains REVERT: A 12 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7471 (mp0) REVERT: A 124 ASN cc_start: 0.7718 (t0) cc_final: 0.6802 (p0) REVERT: A 227 ARG cc_start: 0.8371 (tpt-90) cc_final: 0.7315 (tpp-160) REVERT: A 287 ASN cc_start: 0.8089 (p0) cc_final: 0.7827 (p0) REVERT: A 460 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7099 (mtpt) REVERT: A 462 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7061 (t0) REVERT: A 490 LYS cc_start: 0.7871 (mmtm) cc_final: 0.7140 (mmtt) REVERT: B 11 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7038 (t80) REVERT: B 58 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7269 (mt0) REVERT: B 124 ASN cc_start: 0.7432 (t0) cc_final: 0.6540 (p0) REVERT: B 227 ARG cc_start: 0.8337 (tpt-90) cc_final: 0.7370 (tpp-160) REVERT: B 460 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7236 (mtpt) REVERT: B 462 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7223 (t0) REVERT: B 490 LYS cc_start: 0.8013 (mmtm) cc_final: 0.7197 (mmtt) REVERT: C 10 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7412 (tp) REVERT: C 11 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.7888 (t80) REVERT: C 124 ASN cc_start: 0.7590 (t0) cc_final: 0.6749 (p0) REVERT: C 227 ARG cc_start: 0.8329 (tpt-90) cc_final: 0.7304 (tpp-160) REVERT: C 460 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7197 (mtpt) REVERT: C 462 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7047 (t0) REVERT: C 490 LYS cc_start: 0.7966 (mmtm) cc_final: 0.7214 (mmtt) REVERT: D 11 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8116 (t80) REVERT: D 12 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7510 (mp0) REVERT: D 124 ASN cc_start: 0.7627 (t0) cc_final: 0.6697 (p0) REVERT: D 227 ARG cc_start: 0.8371 (tpt-90) cc_final: 0.7319 (tpp-160) REVERT: D 287 ASN cc_start: 0.8087 (p0) cc_final: 0.7830 (p0) REVERT: D 460 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7092 (mtpt) REVERT: D 490 LYS cc_start: 0.7881 (mmtm) cc_final: 0.7144 (mmtt) REVERT: E 11 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.7030 (t80) REVERT: E 58 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7262 (mt0) REVERT: E 124 ASN cc_start: 0.7405 (t0) cc_final: 0.6547 (p0) REVERT: E 227 ARG cc_start: 0.8329 (tpt-90) cc_final: 0.7375 (tpp-160) REVERT: E 460 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7247 (mtpt) REVERT: E 462 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7225 (t0) REVERT: E 490 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7218 (mmtt) REVERT: F 10 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7438 (tp) REVERT: F 11 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7959 (t80) REVERT: F 58 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7516 (mt0) REVERT: F 124 ASN cc_start: 0.7560 (t0) cc_final: 0.6775 (p0) REVERT: F 227 ARG cc_start: 0.8368 (tpt-90) cc_final: 0.7338 (tpp-160) REVERT: F 460 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7179 (mtpt) REVERT: F 462 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7059 (t0) REVERT: F 490 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7227 (mmtt) outliers start: 52 outliers final: 16 residues processed: 235 average time/residue: 0.6502 time to fit residues: 178.9978 Evaluate side-chains 227 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 460 LYS Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 462 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 281 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 211 optimal weight: 0.1980 chunk 197 optimal weight: 5.9990 chunk 259 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.151928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123666 restraints weight = 28978.248| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.88 r_work: 0.3319 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26976 Z= 0.138 Angle : 0.454 4.786 36756 Z= 0.254 Chirality : 0.039 0.129 3948 Planarity : 0.004 0.045 4518 Dihedral : 14.351 97.290 4250 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.97 % Allowed : 21.07 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.17 (0.15), residues: 3042 helix: 1.80 (0.12), residues: 1722 sheet: -0.19 (0.32), residues: 228 loop : -0.64 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 119 TYR 0.023 0.001 TYR E 238 PHE 0.007 0.001 PHE E 318 TRP 0.010 0.001 TRP E 288 HIS 0.002 0.001 HIS D 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (26976) covalent geometry : angle 0.45377 / 0.25 (36756) hydrogen bonds : bond 0.04327 / 2.90 ( 1243) hydrogen bonds : angle 3.95099 / 2.86 ( 3513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 192 time to evaluate : 1.034 Fit side-chains REVERT: A 11 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8091 (t80) REVERT: A 12 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7496 (mp0) REVERT: A 124 ASN cc_start: 0.7783 (t0) cc_final: 0.6884 (p0) REVERT: A 227 ARG cc_start: 0.8426 (tpt-90) cc_final: 0.7389 (tpp-160) REVERT: A 287 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7880 (p0) REVERT: A 460 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7189 (mtpt) REVERT: A 462 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7088 (t0) REVERT: A 490 LYS cc_start: 0.7932 (mmtm) cc_final: 0.7213 (mmtt) REVERT: B 11 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.7032 (t80) REVERT: B 58 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7359 (mt0) REVERT: B 124 ASN cc_start: 0.7482 (t0) cc_final: 0.6613 (p0) REVERT: B 227 ARG cc_start: 0.8360 (tpt-90) cc_final: 0.7390 (tpp-160) REVERT: B 460 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7303 (mtpt) REVERT: B 462 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7229 (t0) REVERT: B 490 LYS cc_start: 0.8052 (mmtm) cc_final: 0.7240 (mmtt) REVERT: C 10 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7435 (tp) REVERT: C 11 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.8106 (t80) REVERT: C 124 ASN cc_start: 0.7458 (t0) cc_final: 0.6699 (p0) REVERT: C 227 ARG cc_start: 0.8347 (tpt-90) cc_final: 0.7353 (tpp-160) REVERT: C 462 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7067 (t0) REVERT: C 490 LYS cc_start: 0.8032 (mmtm) cc_final: 0.7348 (mmmt) REVERT: D 12 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7532 (mp0) REVERT: D 124 ASN cc_start: 0.7688 (t0) cc_final: 0.6780 (p0) REVERT: D 227 ARG cc_start: 0.8424 (tpt-90) cc_final: 0.7398 (tpp-160) REVERT: D 287 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7889 (p0) REVERT: D 460 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7185 (mtpt) REVERT: D 462 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7084 (t0) REVERT: D 490 LYS cc_start: 0.7946 (mmtm) cc_final: 0.7220 (mmtt) REVERT: E 11 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.7046 (t80) REVERT: E 124 ASN cc_start: 0.7457 (t0) cc_final: 0.6612 (p0) REVERT: E 227 ARG cc_start: 0.8346 (tpt-90) cc_final: 0.7390 (tpp-160) REVERT: E 460 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7321 (mtpt) REVERT: E 462 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7228 (t0) REVERT: E 490 LYS cc_start: 0.8072 (mmtm) cc_final: 0.7259 (mmtt) REVERT: F 10 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7433 (tp) REVERT: F 11 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8094 (t80) REVERT: F 58 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7520 (mt0) REVERT: F 124 ASN cc_start: 0.7589 (t0) cc_final: 0.6813 (p0) REVERT: F 227 ARG cc_start: 0.8386 (tpt-90) cc_final: 0.7383 (tpp-160) REVERT: F 460 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7239 (mtpt) REVERT: F 462 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7046 (t0) REVERT: F 490 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7351 (mmmt) outliers start: 55 outliers final: 21 residues processed: 231 average time/residue: 0.5743 time to fit residues: 156.9929 Evaluate side-chains 232 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 460 LYS Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 328 GLN Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 462 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 132 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 267 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 269 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 273 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120168 restraints weight = 29015.018| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.87 r_work: 0.3248 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 26976 Z= 0.242 Angle : 0.577 7.145 36756 Z= 0.317 Chirality : 0.045 0.147 3948 Planarity : 0.005 0.048 4518 Dihedral : 14.579 92.079 4250 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.86 % Allowed : 21.17 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.78 (0.15), residues: 3042 helix: 1.42 (0.12), residues: 1698 sheet: -0.16 (0.33), residues: 228 loop : -0.71 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 119 TYR 0.036 0.002 TYR A 238 PHE 0.010 0.002 PHE F 432 TRP 0.010 0.002 TRP A 288 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.24 (26976) covalent geometry : angle 0.57731 / 0.32 (36756) hydrogen bonds : bond 0.05805 / 3.90 ( 1243) hydrogen bonds : angle 4.21025 / 3.05 ( 3513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 194 time to evaluate : 1.028 Fit side-chains REVERT: A 11 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8073 (t80) REVERT: A 12 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7497 (mp0) REVERT: A 124 ASN cc_start: 0.7782 (t0) cc_final: 0.6894 (p0) REVERT: A 227 ARG cc_start: 0.8382 (tpt-90) cc_final: 0.7356 (tpp-160) REVERT: A 287 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7907 (p0) REVERT: A 460 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7243 (mtpt) REVERT: A 462 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7159 (t0) REVERT: A 490 LYS cc_start: 0.7980 (mmtm) cc_final: 0.7325 (mmtt) REVERT: B 10 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7327 (tp) REVERT: B 11 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.7324 (t80) REVERT: B 124 ASN cc_start: 0.7600 (t0) cc_final: 0.6730 (p0) REVERT: B 227 ARG cc_start: 0.8375 (tpt-90) cc_final: 0.7383 (tpp-160) REVERT: B 445 ASP cc_start: 0.8057 (m-30) cc_final: 0.7840 (m-30) REVERT: B 460 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7437 (mtpt) REVERT: B 462 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7284 (t0) REVERT: B 490 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7549 (mmtp) REVERT: C 58 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7526 (mt0) REVERT: C 124 ASN cc_start: 0.7591 (t0) cc_final: 0.6786 (p0) REVERT: C 227 ARG cc_start: 0.8399 (tpt-90) cc_final: 0.7360 (tpp-160) REVERT: C 462 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7137 (t0) REVERT: C 490 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7337 (mmtt) REVERT: D 12 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7540 (mp0) REVERT: D 124 ASN cc_start: 0.7790 (t0) cc_final: 0.6900 (p0) REVERT: D 189 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7651 (m-30) REVERT: D 227 ARG cc_start: 0.8387 (tpt-90) cc_final: 0.7382 (tpp-160) REVERT: D 287 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7908 (p0) REVERT: D 460 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7255 (mtpt) REVERT: D 462 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7154 (t0) REVERT: D 490 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7271 (mmtt) REVERT: E 10 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7348 (tp) REVERT: E 11 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.7286 (t80) REVERT: E 124 ASN cc_start: 0.7567 (t0) cc_final: 0.6704 (p0) REVERT: E 227 ARG cc_start: 0.8370 (tpt-90) cc_final: 0.7379 (tpp-160) REVERT: E 445 ASP cc_start: 0.8023 (m-30) cc_final: 0.7806 (m-30) REVERT: E 460 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7368 (mtpt) REVERT: E 462 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7284 (t0) REVERT: E 490 LYS cc_start: 0.8093 (mmtm) cc_final: 0.7562 (mmtp) REVERT: F 58 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: F 124 ASN cc_start: 0.7625 (t0) cc_final: 0.6831 (p0) REVERT: F 227 ARG cc_start: 0.8437 (tpt-90) cc_final: 0.7393 (tpp-160) REVERT: F 462 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7117 (t0) REVERT: F 490 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7363 (mmtt) outliers start: 52 outliers final: 22 residues processed: 233 average time/residue: 0.5889 time to fit residues: 162.2262 Evaluate side-chains 233 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 460 LYS Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 328 GLN Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 462 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 284 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 223 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 291 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 273 HIS C 273 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.150253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.122093 restraints weight = 28945.087| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.87 r_work: 0.3269 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26976 Z= 0.158 Angle : 0.489 5.435 36756 Z= 0.272 Chirality : 0.041 0.134 3948 Planarity : 0.004 0.049 4518 Dihedral : 14.521 94.862 4250 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.61 % Allowed : 21.64 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.87 (0.15), residues: 3042 helix: 1.53 (0.12), residues: 1704 sheet: -0.20 (0.33), residues: 228 loop : -0.71 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 119 TYR 0.025 0.002 TYR A 238 PHE 0.008 0.001 PHE E 318 TRP 0.011 0.001 TRP C 288 HIS 0.005 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (26976) covalent geometry : angle 0.48911 / 0.27 (36756) hydrogen bonds : bond 0.04760 / 3.20 ( 1243) hydrogen bonds : angle 4.08064 / 2.95 ( 3513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 1.059 Fit side-chains REVERT: A 12 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7483 (mp0) REVERT: A 124 ASN cc_start: 0.7801 (t0) cc_final: 0.6888 (p0) REVERT: A 227 ARG cc_start: 0.8387 (tpt-90) cc_final: 0.7358 (tpp-160) REVERT: A 287 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7904 (p0) REVERT: A 460 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7212 (mtpt) REVERT: A 462 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7147 (t0) REVERT: A 490 LYS cc_start: 0.7915 (mmtm) cc_final: 0.7282 (mmtt) REVERT: B 10 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7277 (tp) REVERT: B 11 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.7190 (t80) REVERT: B 124 ASN cc_start: 0.7630 (t0) cc_final: 0.6716 (p0) REVERT: B 227 ARG cc_start: 0.8357 (tpt-90) cc_final: 0.7376 (tpp-160) REVERT: B 272 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8430 (mt) REVERT: B 301 ARG cc_start: 0.4917 (mtt180) cc_final: 0.4704 (ttm170) REVERT: B 445 ASP cc_start: 0.7998 (m-30) cc_final: 0.7787 (m-30) REVERT: B 460 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7333 (mtpt) REVERT: B 462 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7252 (t0) REVERT: B 490 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7530 (mmtp) REVERT: C 124 ASN cc_start: 0.7539 (t0) cc_final: 0.6748 (p0) REVERT: C 227 ARG cc_start: 0.8389 (tpt-90) cc_final: 0.7351 (tpp-160) REVERT: C 462 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7118 (t0) REVERT: C 490 LYS cc_start: 0.8011 (mmtm) cc_final: 0.7328 (mmtt) REVERT: D 12 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7513 (mp0) REVERT: D 124 ASN cc_start: 0.7843 (t0) cc_final: 0.6932 (p0) REVERT: D 135 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: D 227 ARG cc_start: 0.8386 (tpt-90) cc_final: 0.7373 (tpp-160) REVERT: D 287 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7887 (p0) REVERT: D 460 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7221 (mtpt) REVERT: D 462 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7185 (t0) REVERT: D 490 LYS cc_start: 0.7914 (mmtm) cc_final: 0.7275 (mmtt) REVERT: E 10 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7294 (tp) REVERT: E 11 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.7174 (t80) REVERT: E 124 ASN cc_start: 0.7508 (t0) cc_final: 0.6650 (p0) REVERT: E 227 ARG cc_start: 0.8335 (tpt-90) cc_final: 0.7366 (tpp-160) REVERT: E 272 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8420 (mt) REVERT: E 445 ASP cc_start: 0.7946 (m-30) cc_final: 0.7738 (m-30) REVERT: E 460 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7342 (mtpt) REVERT: E 462 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7244 (t0) REVERT: E 490 LYS cc_start: 0.8062 (mmtm) cc_final: 0.7533 (mmtp) REVERT: F 58 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7508 (mt0) REVERT: F 124 ASN cc_start: 0.7579 (t0) cc_final: 0.6755 (p0) REVERT: F 227 ARG cc_start: 0.8387 (tpt-90) cc_final: 0.7357 (tpp-160) REVERT: F 462 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7088 (t0) REVERT: F 490 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7340 (mmtt) outliers start: 45 outliers final: 19 residues processed: 222 average time/residue: 0.5946 time to fit residues: 155.0655 Evaluate side-chains 222 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 460 LYS Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 462 ASP Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 462 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 162 optimal weight: 4.9990 chunk 294 optimal weight: 10.0000 chunk 286 optimal weight: 0.0000 chunk 191 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 299 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 273 HIS E 273 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.149612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.121508 restraints weight = 28877.135| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.87 r_work: 0.3262 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26976 Z= 0.177 Angle : 0.511 6.466 36756 Z= 0.283 Chirality : 0.042 0.134 3948 Planarity : 0.005 0.047 4518 Dihedral : 14.521 93.694 4250 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.65 % Allowed : 21.60 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.82 (0.15), residues: 3042 helix: 1.46 (0.12), residues: 1704 sheet: -0.23 (0.33), residues: 228 loop : -0.67 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 119 TYR 0.030 0.002 TYR D 238 PHE 0.008 0.001 PHE E 318 TRP 0.010 0.001 TRP F 288 HIS 0.004 0.001 HIS E 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (26976) covalent geometry : angle 0.51081 / 0.28 (36756) hydrogen bonds : bond 0.04992 / 3.36 ( 1243) hydrogen bonds : angle 4.10262 / 2.97 ( 3513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7475.68 seconds wall clock time: 128 minutes 19.03 seconds (7699.03 seconds total)