Starting phenix.real_space_refine on Sat Aug 8 08:00:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21ou_67871/08_2026/21ou_67871.cif Found real_map, /net/cci-nas-00/data/ceres_data/21ou_67871/08_2026/21ou_67871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21ou_67871/08_2026/21ou_67871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21ou_67871/08_2026/21ou_67871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21ou_67871/08_2026/21ou_67871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21ou_67871/08_2026/21ou_67871.map" } resolution = 2.34 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= 0.069 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: 5 Type Number sf(0) Gaussians P 48 5.49 5 S 138 5.16 5 C 16650 2.51 5 N 4446 2.21 5 O 5052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 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: 26334 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4221 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 497} Chain: "B" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4221 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 497} Chain: "C" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4221 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 497} Chain: "D" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4221 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 497} Chain: "E" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4221 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 497} Chain: "F" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4221 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 497} 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: "H" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "I" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "J" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "K" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "L" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Time building chain proxies: 5.11, per 1000 atoms: 0.19 Number of scatterers: 26334 At special positions: 0 Unit cell: (150.36, 137.76, 108.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 48 15.00 O 5052 8.00 N 4446 7.00 C 16650 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: 1.87 Conformation dependent library (CDL) restraints added in 932.5 milliseconds 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5916 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 12 sheets defined 63.7% alpha, 4.9% beta 0 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 3.13 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: 3.592A pdb=" N LYS A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 127 through 139 Processing helix chain 'A' and resid 152 through 157 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: 3.796A pdb=" N ASN A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.759A pdb=" N LYS A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 removed outlier: 3.756A pdb=" N SER A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 4.334A 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) Processing helix chain 'A' and resid 248 through 265 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.615A pdb=" N SER A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.620A pdb=" N LYS A 309 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 333 through 343 removed outlier: 3.570A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 365 removed outlier: 3.671A pdb=" N HIS A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 374 Proline residue: A 370 - end of helix Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.569A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 402 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 462 removed outlier: 3.682A pdb=" N ASP A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 470 removed outlier: 3.593A pdb=" N TYR A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 514 through 519 removed outlier: 3.730A pdb=" N VAL A 518 " --> pdb=" O SER A 514 " (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: 3.591A pdb=" N LYS B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 152 through 157 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: 3.797A pdb=" N ASN B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.759A pdb=" N LYS B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 230 removed outlier: 3.756A pdb=" N SER B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 265 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.615A pdb=" N SER B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.620A pdb=" N LYS B 309 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.570A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 365 removed outlier: 3.671A pdb=" N HIS B 364 " --> pdb=" O ASN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 374 Proline residue: B 370 - end of helix Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.568A pdb=" N VAL B 379 " --> pdb=" O ILE B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 402 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 462 removed outlier: 3.682A pdb=" N ASP B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 470 removed outlier: 3.592A pdb=" N TYR B 470 " --> pdb=" O ASP B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'B' and resid 511 through 513 No H-bonds generated for 'chain 'B' and resid 511 through 513' Processing helix chain 'B' and resid 514 through 519 removed outlier: 3.731A pdb=" N VAL B 518 " --> pdb=" O SER B 514 " (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: 3.592A pdb=" N LYS C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 127 through 139 Processing helix chain 'C' and resid 152 through 157 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: 3.797A pdb=" N ASN C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 199 removed outlier: 3.759A pdb=" N LYS C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 230 removed outlier: 3.756A pdb=" N SER C 214 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA C 223 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 265 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.616A pdb=" N SER C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.620A pdb=" N LYS C 309 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 329 Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.570A pdb=" N VAL C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 365 removed outlier: 3.671A pdb=" N HIS C 364 " --> pdb=" O ASN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 374 Proline residue: C 370 - end of helix Processing helix chain 'C' and resid 375 through 379 removed outlier: 3.569A pdb=" N VAL C 379 " --> pdb=" O ILE C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 402 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 462 removed outlier: 3.682A pdb=" N ASP C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 470 removed outlier: 3.594A pdb=" N TYR C 470 " --> pdb=" O ASP C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 490 through 498 Processing helix chain 'C' and resid 511 through 513 No H-bonds generated for 'chain 'C' and resid 511 through 513' Processing helix chain 'C' and resid 514 through 519 removed outlier: 3.730A pdb=" N VAL C 518 " --> pdb=" O SER C 514 " (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: 3.591A pdb=" N LYS D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 127 through 139 Processing helix chain 'D' and resid 152 through 157 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: 3.797A pdb=" N ASN D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 199 removed outlier: 3.759A pdb=" N LYS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.756A pdb=" N SER D 214 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 4.334A 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) Processing helix chain 'D' and resid 248 through 265 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.616A pdb=" N SER D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.620A pdb=" N LYS D 309 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 329 Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.570A pdb=" N VAL D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 365 removed outlier: 3.670A pdb=" N HIS D 364 " --> pdb=" O ASN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 374 Proline residue: D 370 - end of helix Processing helix chain 'D' and resid 375 through 379 removed outlier: 3.569A pdb=" N VAL D 379 " --> pdb=" O ILE D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 402 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 462 removed outlier: 3.682A pdb=" N ASP D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 470 removed outlier: 3.593A pdb=" N TYR D 470 " --> pdb=" O ASP D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 490 through 498 Processing helix chain 'D' and resid 511 through 513 No H-bonds generated for 'chain 'D' and resid 511 through 513' Processing helix chain 'D' and resid 514 through 519 removed outlier: 3.730A pdb=" N VAL D 518 " --> pdb=" O SER D 514 " (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: 3.591A pdb=" N LYS E 87 " --> pdb=" O LYS E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 101 through 105 Processing helix chain 'E' and resid 127 through 139 Processing helix chain 'E' and resid 152 through 157 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: 3.797A pdb=" N ASN E 177 " --> pdb=" O LYS E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 199 removed outlier: 3.759A pdb=" N LYS E 199 " --> pdb=" O GLN E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 230 removed outlier: 3.757A pdb=" N SER E 214 " --> pdb=" O PRO E 210 " (cutoff:3.500A) removed outlier: 4.334A 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) Processing helix chain 'E' and resid 248 through 265 Processing helix chain 'E' and resid 286 through 295 removed outlier: 3.616A pdb=" N SER E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 309 removed outlier: 3.621A pdb=" N LYS E 309 " --> pdb=" O ASP E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 329 Processing helix chain 'E' and resid 333 through 343 removed outlier: 3.570A pdb=" N VAL E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 365 removed outlier: 3.672A pdb=" N HIS E 364 " --> pdb=" O ASN E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 374 Proline residue: E 370 - end of helix Processing helix chain 'E' and resid 375 through 379 removed outlier: 3.569A pdb=" N VAL E 379 " --> pdb=" O ILE E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 402 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 462 removed outlier: 3.683A pdb=" N ASP E 462 " --> pdb=" O ILE E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 470 removed outlier: 3.593A pdb=" N TYR E 470 " --> pdb=" O ASP E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 480 Processing helix chain 'E' and resid 490 through 498 Processing helix chain 'E' and resid 511 through 513 No H-bonds generated for 'chain 'E' and resid 511 through 513' Processing helix chain 'E' and resid 514 through 519 removed outlier: 3.731A pdb=" N VAL E 518 " --> pdb=" O SER E 514 " (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: 3.591A pdb=" N LYS F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 100 Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 127 through 139 Processing helix chain 'F' and resid 152 through 157 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: 3.796A pdb=" N ASN F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 199 removed outlier: 3.759A pdb=" N LYS F 199 " --> pdb=" O GLN F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 230 removed outlier: 3.756A pdb=" N SER F 214 " --> pdb=" O PRO F 210 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL F 224 " --> pdb=" O ILE F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 265 Processing helix chain 'F' and resid 286 through 295 removed outlier: 3.615A pdb=" N SER F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 309 removed outlier: 3.621A pdb=" N LYS F 309 " --> pdb=" O ASP F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 329 Processing helix chain 'F' and resid 333 through 343 removed outlier: 3.570A pdb=" N VAL F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 365 removed outlier: 3.670A pdb=" N HIS F 364 " --> pdb=" O ASN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 374 Proline residue: F 370 - end of helix Processing helix chain 'F' and resid 375 through 379 removed outlier: 3.569A pdb=" N VAL F 379 " --> pdb=" O ILE F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 402 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 462 removed outlier: 3.681A pdb=" N ASP F 462 " --> pdb=" O ILE F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 470 removed outlier: 3.593A pdb=" N TYR F 470 " --> pdb=" O ASP F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 480 Processing helix chain 'F' and resid 490 through 498 Processing helix chain 'F' and resid 511 through 513 No H-bonds generated for 'chain 'F' and resid 511 through 513' Processing helix chain 'F' and resid 514 through 519 removed outlier: 3.729A pdb=" N VAL F 518 " --> pdb=" O SER F 514 " (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 1285 hydrogen bonds defined for protein. 3657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8421 1.34 - 1.46: 6314 1.46 - 1.58: 12061 1.58 - 1.69: 90 1.69 - 1.81: 192 Bond restraints: 27078 Sorted by residual: bond pdb=" P DA H 2 " pdb=" O5' DA H 2 " ideal model delta sigma weight residual 1.593 1.615 -0.022 1.00e-02 1.00e+04 4.90e+00 bond pdb=" P DA H 3 " pdb=" O5' DA H 3 " ideal model delta sigma weight residual 1.593 1.615 -0.022 1.00e-02 1.00e+04 4.74e+00 bond pdb=" P DA L 1 " pdb=" O5' DA L 1 " ideal model delta sigma weight residual 1.593 1.614 -0.021 1.00e-02 1.00e+04 4.57e+00 bond pdb=" P DA L 5 " pdb=" O5' DA L 5 " ideal model delta sigma weight residual 1.593 1.614 -0.021 1.00e-02 1.00e+04 4.45e+00 bond pdb=" P DA L 3 " pdb=" O5' DA L 3 " ideal model delta sigma weight residual 1.593 1.614 -0.021 1.00e-02 1.00e+04 4.44e+00 ... (remaining 27073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 36235 1.63 - 3.26: 440 3.26 - 4.89: 104 4.89 - 6.52: 73 6.52 - 8.15: 6 Bond angle restraints: 36858 Sorted by residual: angle pdb=" O4' DA L 2 " pdb=" C4' DA L 2 " pdb=" C3' DA L 2 " ideal model delta sigma weight residual 106.00 102.71 3.29 6.00e-01 2.78e+00 3.01e+01 angle pdb=" O4' DA G 3 " pdb=" C4' DA G 3 " pdb=" C3' DA G 3 " ideal model delta sigma weight residual 106.00 103.15 2.85 6.00e-01 2.78e+00 2.25e+01 angle pdb=" O4' DA L 4 " pdb=" C4' DA L 4 " pdb=" C3' DA L 4 " ideal model delta sigma weight residual 106.00 103.64 2.36 6.00e-01 2.78e+00 1.55e+01 angle pdb=" C3' DA L 1 " pdb=" O3' DA L 1 " pdb=" P DA L 2 " ideal model delta sigma weight residual 119.70 124.40 -4.70 1.20e+00 6.94e-01 1.54e+01 angle pdb=" C4' DA G 3 " pdb=" O4' DA G 3 " pdb=" C1' DA G 3 " ideal model delta sigma weight residual 110.10 106.39 3.71 1.00e+00 1.00e+00 1.38e+01 ... (remaining 36853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.96: 15051 30.96 - 61.91: 1024 61.91 - 92.87: 105 92.87 - 123.83: 1 123.83 - 154.79: 1 Dihedral angle restraints: 16182 sinusoidal: 6984 harmonic: 9198 Sorted by residual: dihedral pdb=" C4' DA L 1 " pdb=" C3' DA L 1 " pdb=" O3' DA L 1 " pdb=" P DA L 2 " ideal model delta sinusoidal sigma weight residual 220.00 65.21 154.79 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA ASP B 505 " pdb=" CB ASP B 505 " pdb=" CG ASP B 505 " pdb=" OD1 ASP B 505 " ideal model delta sinusoidal sigma weight residual -30.00 -85.85 55.85 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA ASP C 505 " pdb=" CB ASP C 505 " pdb=" CG ASP C 505 " pdb=" OD1 ASP C 505 " ideal model delta sinusoidal sigma weight residual -30.00 -85.85 55.85 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 16179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 3923 0.127 - 0.253: 1 0.253 - 0.380: 0 0.380 - 0.507: 19 0.507 - 0.634: 29 Chirality restraints: 3972 Sorted by residual: chirality pdb=" P DA L 2 " pdb=" OP1 DA L 2 " pdb=" OP2 DA L 2 " pdb=" O5' DA L 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DA K 4 " pdb=" OP1 DA K 4 " pdb=" OP2 DA K 4 " pdb=" O5' DA K 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.57 2.00e-01 2.50e+01 8.23e+00 chirality pdb=" P DA H 2 " pdb=" OP1 DA H 2 " pdb=" OP2 DA H 2 " pdb=" O5' DA H 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.56 2.00e-01 2.50e+01 7.76e+00 ... (remaining 3969 not shown) Planarity restraints: 4554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 209 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO E 210 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 209 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO D 210 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 210 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 210 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 209 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+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 ... (remaining 4551 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 6 1.90 - 2.65: 124 2.65 - 3.40: 34734 3.40 - 4.15: 64040 4.15 - 4.90: 117513 Nonbonded interactions: 216417 Sorted by model distance: nonbonded pdb=" OH TYR D 125 " pdb=" P DA J 1 " model vdw 1.152 3.400 nonbonded pdb=" OH TYR F 125 " pdb=" P DA K 1 " model vdw 1.158 3.400 nonbonded pdb=" OH TYR A 125 " pdb=" P DA G 1 " model vdw 1.167 3.400 nonbonded pdb=" OH TYR C 125 " pdb=" P DA H 1 " model vdw 1.177 3.400 nonbonded pdb=" OH TYR B 125 " pdb=" P DA I 1 " model vdw 1.217 3.400 ... (remaining 216412 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: 0.08 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: 3.740 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.540 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27078 Z= 0.189 Angle : 0.538 8.148 36858 Z= 0.300 Chirality : 0.068 0.634 3972 Planarity : 0.003 0.042 4554 Dihedral : 19.360 154.786 10266 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.95 % Allowed : 14.69 % Favored : 84.36 % 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 (0.14), residues: 3078 helix: 1.36 (0.12), residues: 1710 sheet: -0.45 (0.31), residues: 246 loop : -0.40 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 54 TYR 0.008 0.001 TYR F 238 PHE 0.006 0.001 PHE E 454 TRP 0.011 0.001 TRP C 363 HIS 0.003 0.000 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.19 (27078) covalent geometry : angle 0.53825 / 0.30 (36858) hydrogen bonds : bond 0.15901 / 10.94 ( 1285) hydrogen bonds : angle 5.21780 / 3.70 ( 3657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 301 time to evaluate : 0.924 Fit side-chains REVERT: A 54 ARG cc_start: 0.7631 (ttp80) cc_final: 0.7281 (ptt-90) REVERT: A 98 GLU cc_start: 0.8670 (mm-30) cc_final: 0.7981 (mp0) REVERT: A 123 MET cc_start: 0.8007 (tpp) cc_final: 0.7750 (mmt) REVERT: A 154 PHE cc_start: 0.5619 (m-80) cc_final: 0.5305 (m-80) REVERT: A 276 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8298 (mtpt) REVERT: A 348 GLU cc_start: 0.7164 (mp0) cc_final: 0.6835 (mm-30) REVERT: A 377 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7157 (pm20) REVERT: A 400 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7422 (tm-30) REVERT: A 427 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 460 LYS cc_start: 0.6931 (mtpp) cc_final: 0.6537 (mptt) REVERT: B 54 ARG cc_start: 0.7483 (ttp80) cc_final: 0.7242 (ptt-90) REVERT: B 98 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8013 (mp0) REVERT: B 126 GLU cc_start: 0.7207 (tt0) cc_final: 0.6812 (tt0) REVERT: B 154 PHE cc_start: 0.5474 (m-80) cc_final: 0.5179 (m-80) REVERT: B 199 LYS cc_start: 0.8270 (ttpp) cc_final: 0.8054 (ttmt) REVERT: B 272 LEU cc_start: 0.8255 (mm) cc_final: 0.8000 (mt) REVERT: B 276 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8265 (mtpt) REVERT: B 377 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7062 (pm20) REVERT: B 386 GLU cc_start: 0.7471 (tt0) cc_final: 0.6992 (tp30) REVERT: B 400 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7321 (tm-30) REVERT: B 450 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7582 (mmmt) REVERT: B 460 LYS cc_start: 0.6962 (mtpp) cc_final: 0.6642 (mptt) REVERT: C 39 PHE cc_start: 0.8434 (t80) cc_final: 0.8149 (t80) REVERT: C 54 ARG cc_start: 0.7517 (ttp80) cc_final: 0.7228 (ptt-90) REVERT: C 97 GLU cc_start: 0.7963 (mp0) cc_final: 0.7514 (mp0) REVERT: C 154 PHE cc_start: 0.5401 (m-80) cc_final: 0.5155 (m-80) REVERT: C 276 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8235 (mtpt) REVERT: C 287 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7663 (p0) REVERT: C 301 ARG cc_start: 0.7447 (mtm180) cc_final: 0.7188 (mtt90) REVERT: C 377 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7285 (pm20) REVERT: C 400 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7303 (tm-30) REVERT: C 427 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7857 (mm-30) REVERT: C 449 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6842 (pm20) REVERT: C 450 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7701 (mmtt) REVERT: C 460 LYS cc_start: 0.6897 (mtpp) cc_final: 0.6578 (mptt) REVERT: D 39 PHE cc_start: 0.8416 (t80) cc_final: 0.8136 (t80) REVERT: D 54 ARG cc_start: 0.7543 (ttp80) cc_final: 0.7224 (ptt-90) REVERT: D 97 GLU cc_start: 0.7950 (mp0) cc_final: 0.7496 (mp0) REVERT: D 154 PHE cc_start: 0.5405 (m-80) cc_final: 0.5163 (m-80) REVERT: D 276 LYS cc_start: 0.8684 (mtmm) cc_final: 0.8250 (mtpt) REVERT: D 287 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7646 (p0) REVERT: D 301 ARG cc_start: 0.7431 (mtm180) cc_final: 0.7176 (mtt90) REVERT: D 377 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7285 (pm20) REVERT: D 400 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7333 (tm-30) REVERT: D 427 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7858 (mm-30) REVERT: D 449 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6872 (pm20) REVERT: D 450 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7692 (mmtt) REVERT: D 460 LYS cc_start: 0.6885 (mtpp) cc_final: 0.6592 (mptt) REVERT: E 54 ARG cc_start: 0.7564 (ttp80) cc_final: 0.7221 (ptt-90) REVERT: E 98 GLU cc_start: 0.8684 (mm-30) cc_final: 0.7998 (mp0) REVERT: E 123 MET cc_start: 0.7989 (tpp) cc_final: 0.7723 (mmt) REVERT: E 154 PHE cc_start: 0.5606 (m-80) cc_final: 0.5290 (m-80) REVERT: E 276 LYS cc_start: 0.8725 (mtmm) cc_final: 0.8299 (mtpt) REVERT: E 348 GLU cc_start: 0.7188 (mp0) cc_final: 0.6858 (mm-30) REVERT: E 377 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7154 (pm20) REVERT: E 400 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7392 (tm-30) REVERT: E 427 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7769 (mm-30) REVERT: E 460 LYS cc_start: 0.6948 (mtpp) cc_final: 0.6549 (mptt) REVERT: F 54 ARG cc_start: 0.7501 (ttp80) cc_final: 0.7159 (ptt-90) REVERT: F 126 GLU cc_start: 0.7323 (tt0) cc_final: 0.6924 (tt0) REVERT: F 154 PHE cc_start: 0.5500 (m-80) cc_final: 0.5225 (m-80) REVERT: F 199 LYS cc_start: 0.8352 (ttpp) cc_final: 0.8140 (ttmt) REVERT: F 272 LEU cc_start: 0.8261 (mm) cc_final: 0.8012 (mt) REVERT: F 276 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8245 (mtpt) REVERT: F 377 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7108 (mp0) REVERT: F 386 GLU cc_start: 0.7422 (tt0) cc_final: 0.6961 (tp30) REVERT: F 400 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7284 (tm-30) REVERT: F 450 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7636 (mmmt) REVERT: F 460 LYS cc_start: 0.6863 (mtpp) cc_final: 0.6565 (mptt) outliers start: 27 outliers final: 5 residues processed: 320 average time/residue: 0.8001 time to fit residues: 288.0185 Evaluate side-chains 298 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 285 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain F residue 450 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS A 324 GLN B 17 HIS B 58 GLN C 17 HIS C 324 GLN D 17 HIS D 324 GLN E 17 HIS E 58 GLN E 324 GLN F 17 HIS F 58 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.154081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127291 restraints weight = 25226.094| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.41 r_work: 0.3367 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.0649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 27078 Z= 0.101 Angle : 0.428 5.066 36858 Z= 0.239 Chirality : 0.038 0.286 3972 Planarity : 0.004 0.046 4554 Dihedral : 15.442 158.329 4102 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.24 % Allowed : 13.28 % Favored : 85.49 % 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: 1.48 (0.15), residues: 3078 helix: 1.80 (0.12), residues: 1770 sheet: 0.05 (0.33), residues: 246 loop : -0.10 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 100 TYR 0.013 0.001 TYR C 498 PHE 0.005 0.001 PHE F 454 TRP 0.007 0.001 TRP A 363 HIS 0.003 0.000 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.10 (27078) covalent geometry : angle 0.42816 / 0.24 (36858) hydrogen bonds : bond 0.04278 / 2.87 ( 1285) hydrogen bonds : angle 4.21133 / 3.01 ( 3657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 299 time to evaluate : 0.990 Fit side-chains REVERT: A 54 ARG cc_start: 0.7726 (ttp80) cc_final: 0.7469 (ptt-90) REVERT: A 75 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7639 (ttt180) REVERT: A 98 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7968 (mp0) REVERT: A 154 PHE cc_start: 0.5747 (m-80) cc_final: 0.5459 (m-80) REVERT: A 276 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8246 (mtpt) REVERT: A 348 GLU cc_start: 0.7085 (mp0) cc_final: 0.6791 (mm-30) REVERT: A 377 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7163 (pm20) REVERT: A 400 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7498 (tm-30) REVERT: A 427 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7801 (mm-30) REVERT: A 460 LYS cc_start: 0.7091 (mtpp) cc_final: 0.6660 (mptt) REVERT: B 75 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7634 (ttp-170) REVERT: B 98 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8038 (mp0) REVERT: B 126 GLU cc_start: 0.6813 (tt0) cc_final: 0.6413 (tt0) REVERT: B 154 PHE cc_start: 0.5665 (m-80) cc_final: 0.5372 (m-80) REVERT: B 276 LYS cc_start: 0.8594 (mtmm) cc_final: 0.8216 (mtpt) REVERT: B 348 GLU cc_start: 0.7036 (mp0) cc_final: 0.6812 (mm-30) REVERT: B 377 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7072 (mp0) REVERT: B 386 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7149 (tp30) REVERT: B 400 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7322 (tm-30) REVERT: B 450 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7107 (mtpt) REVERT: B 460 LYS cc_start: 0.7088 (mtpp) cc_final: 0.6793 (mptt) REVERT: C 39 PHE cc_start: 0.8519 (t80) cc_final: 0.8290 (t80) REVERT: C 97 GLU cc_start: 0.8068 (mp0) cc_final: 0.7655 (mp0) REVERT: C 98 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7937 (mp0) REVERT: C 154 PHE cc_start: 0.5560 (m-80) cc_final: 0.5359 (m-80) REVERT: C 276 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8238 (mtpt) REVERT: C 377 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7315 (pm20) REVERT: C 400 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7399 (tm-30) REVERT: C 427 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7873 (mm-30) REVERT: C 460 LYS cc_start: 0.7093 (mtpp) cc_final: 0.6729 (mptt) REVERT: D 39 PHE cc_start: 0.8494 (t80) cc_final: 0.8232 (t80) REVERT: D 97 GLU cc_start: 0.8051 (mp0) cc_final: 0.7634 (mp0) REVERT: D 98 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7914 (mp0) REVERT: D 276 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8215 (mtpt) REVERT: D 324 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8265 (mt0) REVERT: D 377 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7370 (pm20) REVERT: D 400 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7445 (tm-30) REVERT: D 427 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7887 (mm-30) REVERT: D 460 LYS cc_start: 0.7082 (mtpp) cc_final: 0.6744 (mptt) REVERT: E 54 ARG cc_start: 0.7700 (ttp80) cc_final: 0.7455 (ptt-90) REVERT: E 75 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7600 (ttt180) REVERT: E 98 GLU cc_start: 0.8607 (mm-30) cc_final: 0.7991 (mp0) REVERT: E 123 MET cc_start: 0.8167 (tpp) cc_final: 0.7916 (mmt) REVERT: E 154 PHE cc_start: 0.5752 (m-80) cc_final: 0.5471 (m-80) REVERT: E 276 LYS cc_start: 0.8549 (mtmm) cc_final: 0.8202 (mtpt) REVERT: E 348 GLU cc_start: 0.7101 (mp0) cc_final: 0.6809 (mm-30) REVERT: E 377 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7160 (pm20) REVERT: E 400 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7503 (tm-30) REVERT: E 427 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7800 (mm-30) REVERT: E 460 LYS cc_start: 0.7118 (mtpp) cc_final: 0.6691 (mptt) REVERT: F 54 ARG cc_start: 0.7593 (ttp80) cc_final: 0.7347 (ptt-90) REVERT: F 75 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7647 (ttp-170) REVERT: F 98 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8018 (mp0) REVERT: F 126 GLU cc_start: 0.6917 (tt0) cc_final: 0.6524 (tt0) REVERT: F 154 PHE cc_start: 0.5674 (m-80) cc_final: 0.5407 (m-80) REVERT: F 199 LYS cc_start: 0.8491 (ttpp) cc_final: 0.8283 (ttmt) REVERT: F 276 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8180 (mtpt) REVERT: F 377 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7189 (mp0) REVERT: F 386 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7158 (tp30) REVERT: F 400 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7313 (tm-30) REVERT: F 460 LYS cc_start: 0.7051 (mtpp) cc_final: 0.6737 (mptt) outliers start: 35 outliers final: 20 residues processed: 315 average time/residue: 0.7692 time to fit residues: 273.1661 Evaluate side-chains 312 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 284 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 324 GLN Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 386 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 34 optimal weight: 6.9990 chunk 257 optimal weight: 3.9990 chunk 284 optimal weight: 6.9990 chunk 225 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 242 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 219 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 204 HIS A 324 GLN B 58 GLN B 160 HIS C 204 HIS C 324 GLN D 204 HIS E 58 GLN E 204 HIS E 324 GLN F 58 GLN F 160 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.119870 restraints weight = 24958.153| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.42 r_work: 0.3262 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27078 Z= 0.173 Angle : 0.553 8.667 36858 Z= 0.309 Chirality : 0.043 0.313 3972 Planarity : 0.005 0.050 4554 Dihedral : 15.241 154.793 4070 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.91 % Allowed : 13.31 % Favored : 84.78 % 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: 1.50 (0.15), residues: 3078 helix: 1.79 (0.12), residues: 1752 sheet: 0.05 (0.33), residues: 246 loop : -0.01 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 75 TYR 0.025 0.002 TYR F 238 PHE 0.011 0.002 PHE C 140 TRP 0.008 0.002 TRP D 288 HIS 0.004 0.001 HIS C 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (27078) covalent geometry : angle 0.55261 / 0.31 (36858) hydrogen bonds : bond 0.06509 / 4.36 ( 1285) hydrogen bonds : angle 4.28014 / 3.05 ( 3657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 302 time to evaluate : 0.914 Fit side-chains REVERT: A 54 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7452 (ptt-90) REVERT: A 75 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7566 (ttt180) REVERT: A 98 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8033 (mp0) REVERT: A 154 PHE cc_start: 0.5872 (m-80) cc_final: 0.5573 (m-80) REVERT: A 276 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8235 (mtpt) REVERT: A 348 GLU cc_start: 0.7074 (mp0) cc_final: 0.6817 (mm-30) REVERT: A 377 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7299 (pm20) REVERT: A 400 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7587 (tm-30) REVERT: A 427 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7811 (mm-30) REVERT: A 460 LYS cc_start: 0.7383 (mtpp) cc_final: 0.6954 (mptt) REVERT: B 75 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7659 (ttt180) REVERT: B 98 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8099 (mp0) REVERT: B 126 GLU cc_start: 0.6995 (tt0) cc_final: 0.6493 (tt0) REVERT: B 154 PHE cc_start: 0.5740 (m-80) cc_final: 0.5432 (m-80) REVERT: B 276 LYS cc_start: 0.8696 (mtmm) cc_final: 0.8301 (mtpp) REVERT: B 348 GLU cc_start: 0.7080 (mp0) cc_final: 0.6774 (mm-30) REVERT: B 377 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7279 (pm20) REVERT: B 382 ASP cc_start: 0.6341 (OUTLIER) cc_final: 0.5897 (p0) REVERT: B 400 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7490 (tm-30) REVERT: B 460 LYS cc_start: 0.7301 (mtpp) cc_final: 0.6956 (mptt) REVERT: C 10 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8532 (tp) REVERT: C 39 PHE cc_start: 0.8715 (t80) cc_final: 0.8414 (t80) REVERT: C 97 GLU cc_start: 0.8139 (mp0) cc_final: 0.7750 (mp0) REVERT: C 98 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8010 (mp0) REVERT: C 154 PHE cc_start: 0.5663 (m-80) cc_final: 0.5383 (m-80) REVERT: C 276 LYS cc_start: 0.8702 (mtmm) cc_final: 0.8323 (mtpt) REVERT: C 287 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7739 (p0) REVERT: C 306 ASP cc_start: 0.7168 (m-30) cc_final: 0.6924 (t70) REVERT: C 324 GLN cc_start: 0.8654 (mt0) cc_final: 0.8444 (mt0) REVERT: C 377 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7396 (pm20) REVERT: C 382 ASP cc_start: 0.6538 (OUTLIER) cc_final: 0.6107 (p0) REVERT: C 397 MET cc_start: 0.8691 (tmm) cc_final: 0.8319 (tmm) REVERT: C 400 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7452 (tm-30) REVERT: C 427 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7913 (mm-30) REVERT: C 460 LYS cc_start: 0.7366 (mtpp) cc_final: 0.6998 (mptt) REVERT: D 10 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8527 (tp) REVERT: D 39 PHE cc_start: 0.8700 (t80) cc_final: 0.8399 (t80) REVERT: D 97 GLU cc_start: 0.8128 (mp0) cc_final: 0.7732 (mp0) REVERT: D 98 GLU cc_start: 0.8643 (mm-30) cc_final: 0.7984 (mp0) REVERT: D 276 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8322 (mtpt) REVERT: D 287 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7740 (p0) REVERT: D 382 ASP cc_start: 0.6521 (OUTLIER) cc_final: 0.6081 (p0) REVERT: D 400 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7442 (tm-30) REVERT: D 427 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7929 (mm-30) REVERT: D 460 LYS cc_start: 0.7367 (mtpp) cc_final: 0.6998 (mptt) REVERT: E 54 ARG cc_start: 0.7732 (ttp80) cc_final: 0.7458 (ptt-90) REVERT: E 75 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7564 (ttt180) REVERT: E 98 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8051 (mp0) REVERT: E 154 PHE cc_start: 0.5848 (m-80) cc_final: 0.5550 (m-80) REVERT: E 276 LYS cc_start: 0.8630 (mtmm) cc_final: 0.8221 (mtpt) REVERT: E 348 GLU cc_start: 0.7076 (mp0) cc_final: 0.6808 (mm-30) REVERT: E 377 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7277 (pm20) REVERT: E 400 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7583 (tm-30) REVERT: E 427 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7799 (mm-30) REVERT: E 460 LYS cc_start: 0.7324 (mtpp) cc_final: 0.6882 (mptt) REVERT: F 54 ARG cc_start: 0.7650 (ttp80) cc_final: 0.7377 (ptt-90) REVERT: F 75 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7640 (ttt180) REVERT: F 126 GLU cc_start: 0.7298 (tt0) cc_final: 0.6849 (tt0) REVERT: F 154 PHE cc_start: 0.5753 (m-80) cc_final: 0.5465 (m-80) REVERT: F 199 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8502 (ttmt) REVERT: F 276 LYS cc_start: 0.8694 (mtmm) cc_final: 0.8253 (mtpt) REVERT: F 377 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7250 (pm20) REVERT: F 382 ASP cc_start: 0.6295 (OUTLIER) cc_final: 0.5849 (p0) REVERT: F 400 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7516 (tm-30) REVERT: F 460 LYS cc_start: 0.7308 (mtpp) cc_final: 0.6945 (mptt) outliers start: 54 outliers final: 18 residues processed: 338 average time/residue: 0.7044 time to fit residues: 270.1715 Evaluate side-chains 325 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 295 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 382 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 264 optimal weight: 0.5980 chunk 134 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 294 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 193 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN B 58 GLN B 353 GLN D 324 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN F 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.146499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118335 restraints weight = 24652.811| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.48 r_work: 0.3238 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27078 Z= 0.182 Angle : 0.568 5.650 36858 Z= 0.319 Chirality : 0.044 0.326 3972 Planarity : 0.005 0.047 4554 Dihedral : 14.712 154.008 4062 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.98 % Allowed : 13.38 % Favored : 84.64 % 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: 1.32 (0.15), residues: 3078 helix: 1.67 (0.12), residues: 1752 sheet: -0.01 (0.32), residues: 246 loop : -0.12 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 100 TYR 0.026 0.002 TYR B 238 PHE 0.013 0.002 PHE C 140 TRP 0.010 0.002 TRP B 471 HIS 0.005 0.001 HIS F 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (27078) covalent geometry : angle 0.56791 / 0.32 (36858) hydrogen bonds : bond 0.06703 / 4.49 ( 1285) hydrogen bonds : angle 4.35880 / 3.10 ( 3657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 312 time to evaluate : 0.925 Fit side-chains REVERT: A 54 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7456 (ptt-90) REVERT: A 98 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8024 (mp0) REVERT: A 154 PHE cc_start: 0.5938 (m-80) cc_final: 0.5601 (m-80) REVERT: A 276 LYS cc_start: 0.8701 (mtmm) cc_final: 0.8310 (mtpt) REVERT: A 348 GLU cc_start: 0.7120 (mp0) cc_final: 0.6895 (mm-30) REVERT: A 377 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7314 (pm20) REVERT: A 400 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7590 (tm-30) REVERT: A 427 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7956 (mm-30) REVERT: A 450 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7201 (mtpt) REVERT: A 460 LYS cc_start: 0.7380 (mtpp) cc_final: 0.6956 (mptt) REVERT: B 75 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7674 (ttp-170) REVERT: B 126 GLU cc_start: 0.7228 (tt0) cc_final: 0.6777 (tt0) REVERT: B 154 PHE cc_start: 0.5755 (m-80) cc_final: 0.5493 (m-80) REVERT: B 276 LYS cc_start: 0.8711 (mtmm) cc_final: 0.8272 (mtpt) REVERT: B 287 ASN cc_start: 0.8301 (p0) cc_final: 0.8068 (p0) REVERT: B 348 GLU cc_start: 0.7187 (mp0) cc_final: 0.6857 (mm-30) REVERT: B 382 ASP cc_start: 0.6337 (OUTLIER) cc_final: 0.5875 (p0) REVERT: B 400 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7481 (tm-30) REVERT: B 450 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7000 (mmmt) REVERT: B 460 LYS cc_start: 0.7353 (mtpp) cc_final: 0.7012 (mptt) REVERT: C 10 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8531 (tp) REVERT: C 39 PHE cc_start: 0.8782 (t80) cc_final: 0.8451 (t80) REVERT: C 97 GLU cc_start: 0.8178 (mp0) cc_final: 0.7795 (mp0) REVERT: C 98 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8038 (mp0) REVERT: C 154 PHE cc_start: 0.5758 (m-80) cc_final: 0.5444 (m-80) REVERT: C 276 LYS cc_start: 0.8735 (mtmm) cc_final: 0.8368 (mtpt) REVERT: C 287 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7768 (p0) REVERT: C 306 ASP cc_start: 0.7138 (m-30) cc_final: 0.6932 (t70) REVERT: C 382 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.6103 (p0) REVERT: C 397 MET cc_start: 0.8695 (tmm) cc_final: 0.8266 (tmm) REVERT: C 400 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7558 (tm-30) REVERT: C 460 LYS cc_start: 0.7428 (mtpp) cc_final: 0.7088 (mptt) REVERT: D 10 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8533 (tp) REVERT: D 39 PHE cc_start: 0.8798 (t80) cc_final: 0.8468 (t80) REVERT: D 97 GLU cc_start: 0.8173 (mp0) cc_final: 0.7784 (mp0) REVERT: D 98 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8032 (mp0) REVERT: D 276 LYS cc_start: 0.8721 (mtmm) cc_final: 0.8355 (mtpt) REVERT: D 287 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7774 (p0) REVERT: D 324 GLN cc_start: 0.8568 (mt0) cc_final: 0.8291 (mt0) REVERT: D 377 GLU cc_start: 0.7635 (pm20) cc_final: 0.7421 (pm20) REVERT: D 382 ASP cc_start: 0.6568 (OUTLIER) cc_final: 0.6112 (p0) REVERT: D 400 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7437 (tm-30) REVERT: D 460 LYS cc_start: 0.7437 (mtpp) cc_final: 0.7095 (mptt) REVERT: E 54 ARG cc_start: 0.7756 (ttp80) cc_final: 0.7467 (ptt-90) REVERT: E 98 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8047 (mp0) REVERT: E 154 PHE cc_start: 0.5936 (m-80) cc_final: 0.5598 (m-80) REVERT: E 276 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8295 (mtpt) REVERT: E 348 GLU cc_start: 0.7136 (mp0) cc_final: 0.6893 (mm-30) REVERT: E 377 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: E 400 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7605 (tm-30) REVERT: E 427 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7942 (mm-30) REVERT: E 450 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7171 (mtpt) REVERT: E 460 LYS cc_start: 0.7390 (mtpp) cc_final: 0.6974 (mptt) REVERT: F 54 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7403 (ptt-90) REVERT: F 75 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7661 (ttp-170) REVERT: F 126 GLU cc_start: 0.7277 (tt0) cc_final: 0.6824 (tt0) REVERT: F 154 PHE cc_start: 0.5765 (m-80) cc_final: 0.5479 (m-80) REVERT: F 276 LYS cc_start: 0.8709 (mtmm) cc_final: 0.8324 (mtpt) REVERT: F 287 ASN cc_start: 0.8291 (p0) cc_final: 0.8062 (p0) REVERT: F 377 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7294 (pm20) REVERT: F 382 ASP cc_start: 0.6360 (OUTLIER) cc_final: 0.5891 (p0) REVERT: F 400 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7497 (tm-30) REVERT: F 450 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7262 (mmmt) REVERT: F 460 LYS cc_start: 0.7361 (mtpp) cc_final: 0.7017 (mptt) outliers start: 56 outliers final: 18 residues processed: 343 average time/residue: 0.7551 time to fit residues: 293.5711 Evaluate side-chains 335 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 300 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 377 GLU Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 377 GLU Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 450 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 243 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN B 58 GLN B 353 GLN C 324 GLN E 324 GLN F 58 GLN F 353 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120370 restraints weight = 24828.865| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.41 r_work: 0.3268 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 27078 Z= 0.136 Angle : 0.498 5.973 36858 Z= 0.280 Chirality : 0.041 0.332 3972 Planarity : 0.004 0.043 4554 Dihedral : 14.460 152.759 4062 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.66 % Allowed : 13.63 % Favored : 84.71 % 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: 1.47 (0.15), residues: 3078 helix: 1.82 (0.12), residues: 1752 sheet: 0.02 (0.32), residues: 246 loop : -0.11 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 469 TYR 0.019 0.002 TYR E 238 PHE 0.009 0.001 PHE C 140 TRP 0.011 0.002 TRP B 471 HIS 0.003 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (27078) covalent geometry : angle 0.49767 / 0.28 (36858) hydrogen bonds : bond 0.05600 / 3.75 ( 1285) hydrogen bonds : angle 4.22508 / 3.01 ( 3657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 306 time to evaluate : 0.819 Fit side-chains REVERT: A 54 ARG cc_start: 0.7744 (ttp80) cc_final: 0.7463 (ptt-90) REVERT: A 98 GLU cc_start: 0.8636 (mm-30) cc_final: 0.7997 (mp0) REVERT: A 154 PHE cc_start: 0.5905 (m-80) cc_final: 0.5575 (m-80) REVERT: A 348 GLU cc_start: 0.7071 (mp0) cc_final: 0.6842 (mm-30) REVERT: A 377 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7336 (pm20) REVERT: A 400 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7520 (tm-30) REVERT: A 427 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7889 (mm-30) REVERT: A 450 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7150 (mtpt) REVERT: A 460 LYS cc_start: 0.7313 (mtpp) cc_final: 0.6888 (mptt) REVERT: B 126 GLU cc_start: 0.7080 (tt0) cc_final: 0.6540 (tt0) REVERT: B 154 PHE cc_start: 0.5760 (m-80) cc_final: 0.5460 (m-80) REVERT: B 276 LYS cc_start: 0.8684 (mtmm) cc_final: 0.8251 (mtpt) REVERT: B 287 ASN cc_start: 0.8277 (p0) cc_final: 0.8039 (p0) REVERT: B 348 GLU cc_start: 0.7157 (mp0) cc_final: 0.6841 (mm-30) REVERT: B 382 ASP cc_start: 0.6356 (OUTLIER) cc_final: 0.5902 (p0) REVERT: B 400 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7405 (tm-30) REVERT: B 450 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.6908 (mmmt) REVERT: B 460 LYS cc_start: 0.7294 (mtpp) cc_final: 0.6953 (mptt) REVERT: C 10 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8537 (tp) REVERT: C 39 PHE cc_start: 0.8783 (t80) cc_final: 0.8453 (t80) REVERT: C 97 GLU cc_start: 0.8148 (mp0) cc_final: 0.7753 (mp0) REVERT: C 98 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8018 (mp0) REVERT: C 154 PHE cc_start: 0.5728 (m-80) cc_final: 0.5422 (m-80) REVERT: C 276 LYS cc_start: 0.8713 (mtmm) cc_final: 0.8354 (mtpt) REVERT: C 287 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7711 (p0) REVERT: C 306 ASP cc_start: 0.7169 (m-30) cc_final: 0.6927 (t70) REVERT: C 324 GLN cc_start: 0.8592 (mt0) cc_final: 0.8384 (mt0) REVERT: C 382 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6113 (p0) REVERT: C 397 MET cc_start: 0.8646 (tmm) cc_final: 0.8275 (tmm) REVERT: C 400 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7472 (tm-30) REVERT: C 460 LYS cc_start: 0.7359 (mtpp) cc_final: 0.6960 (mmtt) REVERT: C 481 ASP cc_start: 0.8320 (m-30) cc_final: 0.8100 (m-30) REVERT: D 10 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8534 (tp) REVERT: D 39 PHE cc_start: 0.8769 (t80) cc_final: 0.8435 (t80) REVERT: D 97 GLU cc_start: 0.8135 (mp0) cc_final: 0.7741 (mp0) REVERT: D 98 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8003 (mp0) REVERT: D 276 LYS cc_start: 0.8698 (mtmm) cc_final: 0.8340 (mtpt) REVERT: D 287 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7713 (p0) REVERT: D 377 GLU cc_start: 0.7554 (pm20) cc_final: 0.7285 (pm20) REVERT: D 382 ASP cc_start: 0.6571 (OUTLIER) cc_final: 0.6131 (p0) REVERT: D 400 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7495 (tm-30) REVERT: D 460 LYS cc_start: 0.7316 (mtpp) cc_final: 0.6930 (mmtt) REVERT: D 481 ASP cc_start: 0.8318 (m-30) cc_final: 0.8102 (m-30) REVERT: E 54 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7458 (ptt-90) REVERT: E 98 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8034 (mp0) REVERT: E 154 PHE cc_start: 0.5898 (m-80) cc_final: 0.5567 (m-80) REVERT: E 348 GLU cc_start: 0.7067 (mp0) cc_final: 0.6848 (mm-30) REVERT: E 377 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7303 (pm20) REVERT: E 400 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7513 (tm-30) REVERT: E 427 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7878 (mm-30) REVERT: E 450 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7111 (mtpt) REVERT: E 460 LYS cc_start: 0.7311 (mtpp) cc_final: 0.6887 (mptt) REVERT: F 54 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7366 (ptt-90) REVERT: F 126 GLU cc_start: 0.7204 (tt0) cc_final: 0.6730 (tt0) REVERT: F 154 PHE cc_start: 0.5767 (m-80) cc_final: 0.5489 (m-80) REVERT: F 276 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8249 (mtpt) REVERT: F 287 ASN cc_start: 0.8266 (p0) cc_final: 0.8028 (p0) REVERT: F 377 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7273 (pm20) REVERT: F 382 ASP cc_start: 0.6367 (OUTLIER) cc_final: 0.5900 (p0) REVERT: F 400 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7413 (tm-30) REVERT: F 450 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7198 (mmmt) REVERT: F 460 LYS cc_start: 0.7305 (mtpp) cc_final: 0.6961 (mptt) outliers start: 47 outliers final: 17 residues processed: 334 average time/residue: 0.7053 time to fit residues: 267.4204 Evaluate side-chains 327 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 298 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 450 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 291 optimal weight: 0.7980 chunk 27 optimal weight: 0.0000 chunk 161 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 252 optimal weight: 0.7980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN B 58 GLN B 353 GLN E 324 GLN F 58 GLN F 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121615 restraints weight = 24939.755| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.41 r_work: 0.3286 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27078 Z= 0.120 Angle : 0.471 6.153 36858 Z= 0.265 Chirality : 0.040 0.336 3972 Planarity : 0.004 0.046 4554 Dihedral : 14.324 151.782 4062 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.62 % Allowed : 13.84 % Favored : 84.53 % 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: 1.58 (0.15), residues: 3078 helix: 1.92 (0.12), residues: 1752 sheet: 0.01 (0.32), residues: 246 loop : -0.08 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 469 TYR 0.016 0.001 TYR F 238 PHE 0.009 0.001 PHE E 454 TRP 0.010 0.001 TRP F 471 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (27078) covalent geometry : angle 0.47090 / 0.27 (36858) hydrogen bonds : bond 0.05011 / 3.35 ( 1285) hydrogen bonds : angle 4.11807 / 2.93 ( 3657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 305 time to evaluate : 0.940 Fit side-chains REVERT: A 54 ARG cc_start: 0.7718 (ttp80) cc_final: 0.7446 (ptt-90) REVERT: A 98 GLU cc_start: 0.8623 (mm-30) cc_final: 0.7988 (mp0) REVERT: A 154 PHE cc_start: 0.5894 (m-80) cc_final: 0.5575 (m-80) REVERT: A 377 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7357 (pm20) REVERT: A 400 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7526 (tm-30) REVERT: A 427 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 450 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7118 (mtpt) REVERT: A 460 LYS cc_start: 0.7277 (mtpp) cc_final: 0.6819 (mptt) REVERT: B 98 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8029 (mp0) REVERT: B 126 GLU cc_start: 0.6985 (tt0) cc_final: 0.6474 (tt0) REVERT: B 154 PHE cc_start: 0.5759 (m-80) cc_final: 0.5473 (m-80) REVERT: B 276 LYS cc_start: 0.8688 (mtmm) cc_final: 0.8304 (mtpt) REVERT: B 287 ASN cc_start: 0.8236 (p0) cc_final: 0.7996 (p0) REVERT: B 348 GLU cc_start: 0.7136 (mp0) cc_final: 0.6856 (mm-30) REVERT: B 382 ASP cc_start: 0.6335 (OUTLIER) cc_final: 0.5893 (p0) REVERT: B 386 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7183 (tp30) REVERT: B 400 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7384 (tm-30) REVERT: B 450 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.6816 (mmmt) REVERT: B 460 LYS cc_start: 0.7265 (mtpp) cc_final: 0.6921 (mptt) REVERT: C 10 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8549 (tp) REVERT: C 39 PHE cc_start: 0.8765 (t80) cc_final: 0.8438 (t80) REVERT: C 97 GLU cc_start: 0.8123 (mp0) cc_final: 0.7743 (mp0) REVERT: C 98 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8021 (mp0) REVERT: C 154 PHE cc_start: 0.5756 (m-80) cc_final: 0.5446 (m-80) REVERT: C 276 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8332 (mtpt) REVERT: C 287 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7674 (p0) REVERT: C 306 ASP cc_start: 0.7132 (m-30) cc_final: 0.6919 (t70) REVERT: C 324 GLN cc_start: 0.8567 (mt0) cc_final: 0.8353 (mt0) REVERT: C 400 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7452 (tm-30) REVERT: C 460 LYS cc_start: 0.7281 (mtpp) cc_final: 0.6928 (mptt) REVERT: D 10 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8543 (tp) REVERT: D 39 PHE cc_start: 0.8758 (t80) cc_final: 0.8433 (t80) REVERT: D 97 GLU cc_start: 0.8108 (mp0) cc_final: 0.7717 (mp0) REVERT: D 98 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8001 (mp0) REVERT: D 276 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8311 (mtpt) REVERT: D 287 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7680 (p0) REVERT: D 377 GLU cc_start: 0.7511 (pm20) cc_final: 0.7256 (pm20) REVERT: D 400 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7484 (tm-30) REVERT: D 460 LYS cc_start: 0.7276 (mtpp) cc_final: 0.6927 (mptt) REVERT: E 54 ARG cc_start: 0.7704 (ttp80) cc_final: 0.7443 (ptt-90) REVERT: E 98 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8012 (mp0) REVERT: E 154 PHE cc_start: 0.5893 (m-80) cc_final: 0.5570 (m-80) REVERT: E 377 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7314 (pm20) REVERT: E 400 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7563 (tm-30) REVERT: E 427 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7882 (mm-30) REVERT: E 450 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7063 (mtpt) REVERT: E 460 LYS cc_start: 0.7277 (mtpp) cc_final: 0.6818 (mptt) REVERT: F 126 GLU cc_start: 0.7107 (tt0) cc_final: 0.6592 (tt0) REVERT: F 154 PHE cc_start: 0.5744 (m-80) cc_final: 0.5478 (m-80) REVERT: F 276 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8298 (mtpt) REVERT: F 287 ASN cc_start: 0.8216 (p0) cc_final: 0.7995 (p0) REVERT: F 382 ASP cc_start: 0.6355 (OUTLIER) cc_final: 0.5913 (p0) REVERT: F 400 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7384 (tm-30) REVERT: F 460 LYS cc_start: 0.7287 (mtpp) cc_final: 0.6937 (mptt) outliers start: 46 outliers final: 21 residues processed: 333 average time/residue: 0.7087 time to fit residues: 267.5737 Evaluate side-chains 327 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 296 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 450 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 86 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 263 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 50 optimal weight: 0.1980 chunk 213 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN B 353 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN F 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121448 restraints weight = 24948.001| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.41 r_work: 0.3284 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27078 Z= 0.123 Angle : 0.476 6.482 36858 Z= 0.267 Chirality : 0.040 0.350 3972 Planarity : 0.004 0.042 4554 Dihedral : 14.268 151.630 4062 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.55 % Allowed : 14.19 % Favored : 84.25 % 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: 3078 helix: 1.93 (0.12), residues: 1752 sheet: 0.03 (0.32), residues: 246 loop : -0.05 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 237 TYR 0.017 0.001 TYR F 238 PHE 0.008 0.001 PHE D 140 TRP 0.010 0.001 TRP F 471 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (27078) covalent geometry : angle 0.47617 / 0.27 (36858) hydrogen bonds : bond 0.05108 / 3.42 ( 1285) hydrogen bonds : angle 4.10963 / 2.93 ( 3657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 299 time to evaluate : 0.811 Fit side-chains REVERT: A 54 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7449 (ptt-90) REVERT: A 98 GLU cc_start: 0.8618 (mm-30) cc_final: 0.7986 (mp0) REVERT: A 154 PHE cc_start: 0.5908 (m-80) cc_final: 0.5582 (m-80) REVERT: A 377 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7332 (pm20) REVERT: A 400 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7568 (tm-30) REVERT: A 427 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7798 (mm-30) REVERT: A 460 LYS cc_start: 0.7278 (mtpp) cc_final: 0.6825 (mptt) REVERT: B 126 GLU cc_start: 0.7085 (tt0) cc_final: 0.6563 (tt0) REVERT: B 154 PHE cc_start: 0.5771 (m-80) cc_final: 0.5486 (m-80) REVERT: B 276 LYS cc_start: 0.8690 (mtmm) cc_final: 0.8269 (mtpt) REVERT: B 287 ASN cc_start: 0.8271 (p0) cc_final: 0.8053 (p0) REVERT: B 382 ASP cc_start: 0.6349 (OUTLIER) cc_final: 0.5908 (p0) REVERT: B 400 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7384 (tm-30) REVERT: B 460 LYS cc_start: 0.7272 (mtpp) cc_final: 0.6931 (mptt) REVERT: C 10 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8521 (tp) REVERT: C 39 PHE cc_start: 0.8762 (t80) cc_final: 0.8434 (t80) REVERT: C 97 GLU cc_start: 0.8125 (mp0) cc_final: 0.7746 (mp0) REVERT: C 98 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8020 (mp0) REVERT: C 154 PHE cc_start: 0.5751 (m-80) cc_final: 0.5444 (m-80) REVERT: C 276 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8332 (mtpt) REVERT: C 287 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7692 (p0) REVERT: C 306 ASP cc_start: 0.7156 (m-30) cc_final: 0.6924 (t70) REVERT: C 324 GLN cc_start: 0.8566 (mt0) cc_final: 0.8337 (mt0) REVERT: C 382 ASP cc_start: 0.6571 (OUTLIER) cc_final: 0.6133 (p0) REVERT: C 400 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7469 (tm-30) REVERT: C 460 LYS cc_start: 0.7296 (mtpp) cc_final: 0.6946 (mptt) REVERT: D 10 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8518 (tp) REVERT: D 39 PHE cc_start: 0.8756 (t80) cc_final: 0.8430 (t80) REVERT: D 97 GLU cc_start: 0.8107 (mp0) cc_final: 0.7726 (mp0) REVERT: D 98 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8002 (mp0) REVERT: D 276 LYS cc_start: 0.8669 (mtmm) cc_final: 0.8328 (mtpt) REVERT: D 287 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7695 (p0) REVERT: D 377 GLU cc_start: 0.7528 (pm20) cc_final: 0.7252 (pm20) REVERT: D 382 ASP cc_start: 0.6570 (OUTLIER) cc_final: 0.6133 (p0) REVERT: D 400 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7496 (tm-30) REVERT: D 460 LYS cc_start: 0.7293 (mtpp) cc_final: 0.6936 (mptt) REVERT: E 54 ARG cc_start: 0.7720 (ttp80) cc_final: 0.7444 (ptt-90) REVERT: E 98 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8002 (mp0) REVERT: E 154 PHE cc_start: 0.5893 (m-80) cc_final: 0.5568 (m-80) REVERT: E 377 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7303 (pm20) REVERT: E 400 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7552 (tm-30) REVERT: E 427 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7791 (mm-30) REVERT: E 460 LYS cc_start: 0.7280 (mtpp) cc_final: 0.6827 (mptt) REVERT: F 75 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7626 (ttp-170) REVERT: F 126 GLU cc_start: 0.7121 (tt0) cc_final: 0.6612 (tt0) REVERT: F 154 PHE cc_start: 0.5742 (m-80) cc_final: 0.5476 (m-80) REVERT: F 276 LYS cc_start: 0.8696 (mtmm) cc_final: 0.8274 (mtpt) REVERT: F 382 ASP cc_start: 0.6377 (OUTLIER) cc_final: 0.5937 (p0) REVERT: F 400 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7384 (tm-30) REVERT: F 460 LYS cc_start: 0.7308 (mtpp) cc_final: 0.6941 (mptt) outliers start: 44 outliers final: 24 residues processed: 328 average time/residue: 0.6948 time to fit residues: 258.4213 Evaluate side-chains 331 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 298 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 382 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 266 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN B 204 HIS B 353 GLN E 324 GLN F 58 GLN F 204 HIS F 353 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.146114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118797 restraints weight = 24942.326| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.41 r_work: 0.3247 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27078 Z= 0.179 Angle : 0.563 6.447 36858 Z= 0.315 Chirality : 0.043 0.346 3972 Planarity : 0.005 0.048 4554 Dihedral : 14.278 151.522 4062 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.77 % Allowed : 13.95 % Favored : 84.29 % 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: 1.56 (0.15), residues: 3078 helix: 1.82 (0.12), residues: 1716 sheet: 0.02 (0.32), residues: 246 loop : 0.14 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 100 TYR 0.028 0.002 TYR F 238 PHE 0.012 0.002 PHE D 140 TRP 0.008 0.002 TRP B 363 HIS 0.004 0.001 HIS F 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (27078) covalent geometry : angle 0.56268 / 0.32 (36858) hydrogen bonds : bond 0.06512 / 4.36 ( 1285) hydrogen bonds : angle 4.29420 / 3.06 ( 3657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 308 time to evaluate : 0.990 Fit side-chains REVERT: A 54 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7423 (ptt-90) REVERT: A 75 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7609 (ttt180) REVERT: A 98 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8013 (mp0) REVERT: A 154 PHE cc_start: 0.5929 (m-80) cc_final: 0.5602 (m-80) REVERT: A 377 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7342 (pm20) REVERT: A 400 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7576 (tm-30) REVERT: A 427 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7911 (mm-30) REVERT: A 450 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7183 (mtpt) REVERT: A 460 LYS cc_start: 0.7316 (mtpp) cc_final: 0.6883 (mptt) REVERT: B 75 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7688 (ttp-170) REVERT: B 126 GLU cc_start: 0.7211 (tt0) cc_final: 0.6764 (tt0) REVERT: B 154 PHE cc_start: 0.5786 (m-80) cc_final: 0.5495 (m-80) REVERT: B 276 LYS cc_start: 0.8720 (mtmm) cc_final: 0.8292 (mtpp) REVERT: B 287 ASN cc_start: 0.8311 (p0) cc_final: 0.8103 (p0) REVERT: B 382 ASP cc_start: 0.6426 (OUTLIER) cc_final: 0.5961 (p0) REVERT: B 400 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7429 (tm-30) REVERT: B 460 LYS cc_start: 0.7320 (mtpp) cc_final: 0.6968 (mptt) REVERT: C 10 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8536 (tp) REVERT: C 39 PHE cc_start: 0.8800 (t80) cc_final: 0.8471 (t80) REVERT: C 97 GLU cc_start: 0.8154 (mp0) cc_final: 0.7770 (mp0) REVERT: C 98 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8008 (mp0) REVERT: C 154 PHE cc_start: 0.5752 (m-80) cc_final: 0.5433 (m-80) REVERT: C 276 LYS cc_start: 0.8696 (mtmm) cc_final: 0.8348 (mtpt) REVERT: C 287 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7765 (p0) REVERT: C 306 ASP cc_start: 0.7186 (m-30) cc_final: 0.6943 (t70) REVERT: C 324 GLN cc_start: 0.8626 (mt0) cc_final: 0.8398 (mt0) REVERT: C 400 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7547 (tm-30) REVERT: C 460 LYS cc_start: 0.7412 (mtpp) cc_final: 0.7053 (mptt) REVERT: D 10 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8534 (tp) REVERT: D 39 PHE cc_start: 0.8792 (t80) cc_final: 0.8465 (t80) REVERT: D 97 GLU cc_start: 0.8140 (mp0) cc_final: 0.7763 (mp0) REVERT: D 98 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8014 (mp0) REVERT: D 276 LYS cc_start: 0.8690 (mtmm) cc_final: 0.8339 (mtpt) REVERT: D 287 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7761 (p0) REVERT: D 400 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7460 (tm-30) REVERT: D 460 LYS cc_start: 0.7422 (mtpp) cc_final: 0.7058 (mptt) REVERT: E 54 ARG cc_start: 0.7681 (ttp80) cc_final: 0.7413 (ptt-90) REVERT: E 75 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7599 (ttt180) REVERT: E 98 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8031 (mp0) REVERT: E 154 PHE cc_start: 0.5919 (m-80) cc_final: 0.5590 (m-80) REVERT: E 287 ASN cc_start: 0.8372 (p0) cc_final: 0.8120 (p0) REVERT: E 377 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7313 (pm20) REVERT: E 400 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7566 (tm-30) REVERT: E 427 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7903 (mm-30) REVERT: E 450 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7153 (mtpt) REVERT: E 460 LYS cc_start: 0.7319 (mtpp) cc_final: 0.6896 (mptt) REVERT: F 75 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7673 (ttp-170) REVERT: F 126 GLU cc_start: 0.7264 (tt0) cc_final: 0.6818 (tt0) REVERT: F 154 PHE cc_start: 0.5817 (m-80) cc_final: 0.5538 (m-80) REVERT: F 276 LYS cc_start: 0.8713 (mtmm) cc_final: 0.8288 (mtpp) REVERT: F 377 GLU cc_start: 0.7429 (pm20) cc_final: 0.7156 (pm20) REVERT: F 382 ASP cc_start: 0.6430 (OUTLIER) cc_final: 0.5975 (p0) REVERT: F 400 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7441 (tm-30) REVERT: F 460 LYS cc_start: 0.7333 (mtpp) cc_final: 0.6982 (mptt) outliers start: 50 outliers final: 22 residues processed: 337 average time/residue: 0.7422 time to fit residues: 282.4918 Evaluate side-chains 337 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 303 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 382 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 chunk 211 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN B 353 GLN E 324 GLN F 58 GLN F 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121151 restraints weight = 25047.403| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.41 r_work: 0.3279 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27078 Z= 0.121 Angle : 0.482 6.665 36858 Z= 0.270 Chirality : 0.040 0.351 3972 Planarity : 0.004 0.044 4554 Dihedral : 14.246 151.195 4062 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.34 % Allowed : 14.51 % Favored : 84.15 % 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: 1.72 (0.15), residues: 3078 helix: 1.99 (0.12), residues: 1716 sheet: 0.03 (0.32), residues: 246 loop : 0.16 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 119 TYR 0.016 0.001 TYR F 238 PHE 0.009 0.001 PHE E 454 TRP 0.011 0.002 TRP F 471 HIS 0.003 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (27078) covalent geometry : angle 0.48155 / 0.27 (36858) hydrogen bonds : bond 0.05173 / 3.47 ( 1285) hydrogen bonds : angle 4.15030 / 2.95 ( 3657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 302 time to evaluate : 1.029 Fit side-chains REVERT: A 54 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7429 (ptt-90) REVERT: A 98 GLU cc_start: 0.8622 (mm-30) cc_final: 0.7987 (mp0) REVERT: A 154 PHE cc_start: 0.5923 (m-80) cc_final: 0.5591 (m-80) REVERT: A 377 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7372 (pm20) REVERT: A 400 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7557 (tm-30) REVERT: A 427 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7884 (mm-30) REVERT: A 450 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7085 (mtpt) REVERT: A 460 LYS cc_start: 0.7267 (mtpp) cc_final: 0.6834 (mptt) REVERT: B 126 GLU cc_start: 0.7059 (tt0) cc_final: 0.6521 (tt0) REVERT: B 154 PHE cc_start: 0.5759 (m-80) cc_final: 0.5468 (m-80) REVERT: B 276 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8261 (mtpt) REVERT: B 377 GLU cc_start: 0.7401 (pm20) cc_final: 0.7165 (pm20) REVERT: B 382 ASP cc_start: 0.6404 (OUTLIER) cc_final: 0.5962 (p0) REVERT: B 386 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: B 400 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7411 (tm-30) REVERT: B 460 LYS cc_start: 0.7275 (mtpp) cc_final: 0.6933 (mptt) REVERT: C 10 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8530 (tp) REVERT: C 39 PHE cc_start: 0.8777 (t80) cc_final: 0.8402 (t80) REVERT: C 97 GLU cc_start: 0.8123 (mp0) cc_final: 0.7753 (mp0) REVERT: C 98 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8015 (mp0) REVERT: C 154 PHE cc_start: 0.5753 (m-80) cc_final: 0.5440 (m-80) REVERT: C 276 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8328 (mtpt) REVERT: C 287 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7702 (p0) REVERT: C 306 ASP cc_start: 0.7156 (m-30) cc_final: 0.6923 (t70) REVERT: C 324 GLN cc_start: 0.8547 (mt0) cc_final: 0.8341 (mt0) REVERT: C 400 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7495 (tm-30) REVERT: C 460 LYS cc_start: 0.7300 (mtpp) cc_final: 0.6960 (mptt) REVERT: D 10 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8527 (tp) REVERT: D 39 PHE cc_start: 0.8771 (t80) cc_final: 0.8400 (t80) REVERT: D 97 GLU cc_start: 0.8111 (mp0) cc_final: 0.7719 (mp0) REVERT: D 98 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8002 (mp0) REVERT: D 276 LYS cc_start: 0.8663 (mtmm) cc_final: 0.8321 (mtpt) REVERT: D 287 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7694 (p0) REVERT: D 400 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7496 (tm-30) REVERT: D 460 LYS cc_start: 0.7301 (mtpp) cc_final: 0.6954 (mptt) REVERT: E 54 ARG cc_start: 0.7671 (ttp80) cc_final: 0.7422 (ptt-90) REVERT: E 98 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8014 (mp0) REVERT: E 154 PHE cc_start: 0.5917 (m-80) cc_final: 0.5585 (m-80) REVERT: E 287 ASN cc_start: 0.8288 (p0) cc_final: 0.8029 (p0) REVERT: E 377 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7327 (pm20) REVERT: E 400 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7517 (tm-30) REVERT: E 427 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7885 (mm-30) REVERT: E 450 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7066 (mtpt) REVERT: E 460 LYS cc_start: 0.7262 (mtpp) cc_final: 0.6832 (mptt) REVERT: F 126 GLU cc_start: 0.7114 (tt0) cc_final: 0.6586 (tt0) REVERT: F 154 PHE cc_start: 0.5770 (m-80) cc_final: 0.5494 (m-80) REVERT: F 276 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8263 (mtpt) REVERT: F 377 GLU cc_start: 0.7434 (pm20) cc_final: 0.7156 (pm20) REVERT: F 382 ASP cc_start: 0.6411 (OUTLIER) cc_final: 0.5974 (p0) REVERT: F 400 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7427 (tm-30) REVERT: F 460 LYS cc_start: 0.7280 (mtpp) cc_final: 0.6933 (mptt) outliers start: 38 outliers final: 23 residues processed: 327 average time/residue: 0.7903 time to fit residues: 291.9396 Evaluate side-chains 330 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 287 ASN Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 450 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 22 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 257 optimal weight: 0.0030 chunk 110 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 212 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 209 optimal weight: 0.0570 overall best weight: 0.5510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN B 58 GLN B 353 GLN E 324 GLN F 58 GLN F 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.151504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124672 restraints weight = 25025.939| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.40 r_work: 0.3327 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 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 : 0.002 0.041 27078 Z= 0.098 Angle : 0.439 7.162 36858 Z= 0.245 Chirality : 0.038 0.359 3972 Planarity : 0.004 0.045 4554 Dihedral : 14.168 150.649 4062 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.09 % Allowed : 14.87 % Favored : 84.04 % 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: 1.70 (0.15), residues: 3078 helix: 2.04 (0.12), residues: 1764 sheet: 0.04 (0.32), residues: 246 loop : -0.10 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 119 TYR 0.011 0.001 TYR F 65 PHE 0.008 0.001 PHE E 454 TRP 0.013 0.002 TRP F 471 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.10 (27078) covalent geometry : angle 0.43853 / 0.24 (36858) hydrogen bonds : bond 0.03943 / 2.64 ( 1285) hydrogen bonds : angle 3.97868 / 2.83 ( 3657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 299 time to evaluate : 0.990 Fit side-chains REVERT: A 54 ARG cc_start: 0.7663 (ttp80) cc_final: 0.7417 (ptt-90) REVERT: A 98 GLU cc_start: 0.8587 (mm-30) cc_final: 0.7972 (mp0) REVERT: A 154 PHE cc_start: 0.5890 (m-80) cc_final: 0.5588 (m-80) REVERT: A 276 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8229 (mtpt) REVERT: A 377 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7349 (pm20) REVERT: A 400 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 427 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7893 (mm-30) REVERT: A 460 LYS cc_start: 0.7049 (mtpp) cc_final: 0.6622 (mptt) REVERT: B 24 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7859 (mtmt) REVERT: B 126 GLU cc_start: 0.6951 (tt0) cc_final: 0.6435 (tt0) REVERT: B 154 PHE cc_start: 0.5709 (m-80) cc_final: 0.5438 (m-80) REVERT: B 276 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8271 (mtpt) REVERT: B 386 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7180 (tp30) REVERT: B 400 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7303 (tm-30) REVERT: B 460 LYS cc_start: 0.7172 (mtpp) cc_final: 0.6846 (mptt) REVERT: C 39 PHE cc_start: 0.8697 (t80) cc_final: 0.8351 (t80) REVERT: C 97 GLU cc_start: 0.8057 (mp0) cc_final: 0.7667 (mp0) REVERT: C 98 GLU cc_start: 0.8607 (mm-30) cc_final: 0.7985 (mp0) REVERT: C 154 PHE cc_start: 0.5738 (m-80) cc_final: 0.5434 (m-80) REVERT: C 276 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8287 (mtpt) REVERT: C 324 GLN cc_start: 0.8511 (mt0) cc_final: 0.8304 (mt0) REVERT: C 400 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7466 (tm-30) REVERT: C 460 LYS cc_start: 0.7153 (mtpp) cc_final: 0.6820 (mptt) REVERT: D 39 PHE cc_start: 0.8695 (t80) cc_final: 0.8359 (t80) REVERT: D 97 GLU cc_start: 0.8034 (mp0) cc_final: 0.7644 (mp0) REVERT: D 98 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7964 (mp0) REVERT: D 276 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8274 (mtpt) REVERT: D 400 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7461 (tm-30) REVERT: D 460 LYS cc_start: 0.7156 (mtpp) cc_final: 0.6816 (mptt) REVERT: E 54 ARG cc_start: 0.7617 (ttp80) cc_final: 0.7395 (ptt-90) REVERT: E 98 GLU cc_start: 0.8596 (mm-30) cc_final: 0.7982 (mp0) REVERT: E 154 PHE cc_start: 0.5875 (m-80) cc_final: 0.5574 (m-80) REVERT: E 276 LYS cc_start: 0.8563 (mtmm) cc_final: 0.8214 (mtpt) REVERT: E 287 ASN cc_start: 0.8149 (p0) cc_final: 0.7870 (p0) REVERT: E 377 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7319 (pm20) REVERT: E 400 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7506 (tm-30) REVERT: E 427 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7900 (mm-30) REVERT: E 460 LYS cc_start: 0.7046 (mtpp) cc_final: 0.6617 (mptt) REVERT: F 126 GLU cc_start: 0.6937 (tt0) cc_final: 0.6448 (tt0) REVERT: F 154 PHE cc_start: 0.5762 (m-80) cc_final: 0.5499 (m-80) REVERT: F 276 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8268 (mtpt) REVERT: F 400 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7321 (tm-30) REVERT: F 460 LYS cc_start: 0.7172 (mtpp) cc_final: 0.6849 (mptt) outliers start: 31 outliers final: 16 residues processed: 318 average time/residue: 0.7611 time to fit residues: 273.2341 Evaluate side-chains 310 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 293 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 264 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 231 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 238 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 324 GLN B 58 GLN B 353 GLN E 58 GLN E 324 GLN F 58 GLN F 353 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.149520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122434 restraints weight = 24942.467| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.41 r_work: 0.3296 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27078 Z= 0.119 Angle : 0.467 6.322 36858 Z= 0.262 Chirality : 0.039 0.355 3972 Planarity : 0.004 0.042 4554 Dihedral : 14.120 150.570 4062 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.85 % Allowed : 15.01 % Favored : 84.15 % 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: 1.69 (0.15), residues: 3078 helix: 2.02 (0.12), residues: 1764 sheet: 0.09 (0.32), residues: 246 loop : -0.08 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 100 TYR 0.016 0.001 TYR E 238 PHE 0.008 0.001 PHE E 454 TRP 0.010 0.002 TRP B 471 HIS 0.005 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (27078) covalent geometry : angle 0.46737 / 0.26 (36858) hydrogen bonds : bond 0.04793 / 3.21 ( 1285) hydrogen bonds : angle 4.03509 / 2.87 ( 3657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9334.52 seconds wall clock time: 159 minutes 26.22 seconds (9566.22 seconds total)