Starting phenix.real_space_refine on Mon Sep 30 14:39:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1c_28793/09_2024/8f1c_28793_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1c_28793/09_2024/8f1c_28793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1c_28793/09_2024/8f1c_28793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1c_28793/09_2024/8f1c_28793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1c_28793/09_2024/8f1c_28793_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1c_28793/09_2024/8f1c_28793_trim.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.045 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: 9 Type Number sf(0) Gaussians K 4 8.98 5 Zn 4 6.06 5 P 4 5.49 5 S 68 5.16 5 Cl 4 4.86 5 C 8520 2.51 5 N 2120 2.21 5 O 2208 1.98 5 H 12184 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25116 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 6194 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 21, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 88 Unusual residues: {' K': 4, ' ZN': 1, 'POV': 1, 'X9T': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1518 SG CYS A 104 63.879 52.710 75.558 1.00 53.86 S Restraints were copied for chains: B, C, D Time building chain proxies: 16.04, per 1000 atoms: 0.64 Number of scatterers: 25116 At special positions: 0 Unit cell: (135.24, 135.24, 122.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 4 29.99 K 4 19.00 Cl 4 17.00 S 68 16.00 P 4 15.00 O 2208 8.00 N 2120 7.00 C 8520 6.00 H 12184 1.00 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: 6.70 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 77 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 104 " pdb="ZN ZN A 601 " - pdb=" SG CYS D 83 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS A 83 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 104 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS B 83 " pdb="ZN ZN C 601 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 104 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 104 " pdb="ZN ZN D 601 " - pdb=" SG CYS C 83 " 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 4 sheets defined 70.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 removed outlier: 3.975A pdb=" N LEU A 26 " --> pdb=" O TYR A 22 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 22 through 27' Processing helix chain 'A' and resid 32 through 39 removed outlier: 3.540A pdb=" N GLU A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.729A pdb=" N PHE A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 65 " --> pdb=" O PRO A 61 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.703A pdb=" N ASP A 100 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 101 " --> pdb=" O GLU A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.697A pdb=" N TYR A 109 " --> pdb=" O CYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 removed outlier: 3.905A pdb=" N ALA A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 180 removed outlier: 3.869A pdb=" N PHE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 211 removed outlier: 3.914A pdb=" N THR A 211 " --> pdb=" O PHE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 266 removed outlier: 3.620A pdb=" N GLU A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.548A pdb=" N TYR A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 311 removed outlier: 4.456A pdb=" N ASP A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.665A pdb=" N ARG A 320 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.695A pdb=" N ARG A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 Processing helix chain 'A' and resid 341 through 367 Processing helix chain 'A' and resid 377 through 381 removed outlier: 4.179A pdb=" N HIS A 381 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 removed outlier: 4.363A pdb=" N TRP A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 431 through 452 removed outlier: 3.606A pdb=" N ILE A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 removed outlier: 3.974A pdb=" N LEU B 26 " --> pdb=" O TYR B 22 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 22 through 27' Processing helix chain 'B' and resid 32 through 39 removed outlier: 3.540A pdb=" N GLU B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 74 removed outlier: 3.729A pdb=" N PHE B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N HIS B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.703A pdb=" N ASP B 100 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 101 " --> pdb=" O GLU B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 105 through 110 removed outlier: 3.697A pdb=" N TYR B 109 " --> pdb=" O CYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.906A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 180 removed outlier: 3.869A pdb=" N PHE B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 211 removed outlier: 3.913A pdb=" N THR B 211 " --> pdb=" O PHE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 266 removed outlier: 3.619A pdb=" N GLU B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.548A pdb=" N TYR B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 311 removed outlier: 4.456A pdb=" N ASP B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.665A pdb=" N ARG B 320 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.695A pdb=" N ARG B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 Processing helix chain 'B' and resid 341 through 367 Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.179A pdb=" N HIS B 381 " --> pdb=" O ALA B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 399 removed outlier: 4.363A pdb=" N TRP B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 431 through 452 removed outlier: 3.606A pdb=" N ILE B 435 " --> pdb=" O PRO B 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 27 removed outlier: 3.975A pdb=" N LEU C 26 " --> pdb=" O TYR C 22 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG C 27 " --> pdb=" O ARG C 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 22 through 27' Processing helix chain 'C' and resid 32 through 39 removed outlier: 3.540A pdb=" N GLU C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.729A pdb=" N PHE C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C 65 " --> pdb=" O PRO C 61 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.703A pdb=" N ASP C 100 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 105 through 110 removed outlier: 3.697A pdb=" N TYR C 109 " --> pdb=" O CYS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 121 removed outlier: 3.905A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 180 removed outlier: 3.869A pdb=" N PHE C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 211 removed outlier: 3.913A pdb=" N THR C 211 " --> pdb=" O PHE C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 266 removed outlier: 3.619A pdb=" N GLU C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'C' and resid 278 through 285 Processing helix chain 'C' and resid 286 through 294 removed outlier: 3.548A pdb=" N TYR C 290 " --> pdb=" O ILE C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 311 removed outlier: 4.456A pdb=" N ASP C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.664A pdb=" N ARG C 320 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.695A pdb=" N ARG C 326 " --> pdb=" O PHE C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 341 Processing helix chain 'C' and resid 341 through 367 Processing helix chain 'C' and resid 377 through 381 removed outlier: 4.178A pdb=" N HIS C 381 " --> pdb=" O ALA C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 399 removed outlier: 4.364A pdb=" N TRP C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 431 through 452 removed outlier: 3.606A pdb=" N ILE C 435 " --> pdb=" O PRO C 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 removed outlier: 3.974A pdb=" N LEU D 26 " --> pdb=" O TYR D 22 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 22 through 27' Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.540A pdb=" N GLU D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 74 removed outlier: 3.729A pdb=" N PHE D 64 " --> pdb=" O HIS D 60 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA D 65 " --> pdb=" O PRO D 61 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.705A pdb=" N ASP D 100 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 101 " --> pdb=" O GLU D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 105 through 110 removed outlier: 3.697A pdb=" N TYR D 109 " --> pdb=" O CYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.905A pdb=" N ALA D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 180 removed outlier: 3.869A pdb=" N PHE D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 211 removed outlier: 3.913A pdb=" N THR D 211 " --> pdb=" O PHE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 266 removed outlier: 3.619A pdb=" N GLU D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 276 Processing helix chain 'D' and resid 278 through 285 Processing helix chain 'D' and resid 286 through 294 removed outlier: 3.548A pdb=" N TYR D 290 " --> pdb=" O ILE D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 311 removed outlier: 4.456A pdb=" N ASP D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.665A pdb=" N ARG D 320 " --> pdb=" O ARG D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.695A pdb=" N ARG D 326 " --> pdb=" O PHE D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 Processing helix chain 'D' and resid 341 through 367 Processing helix chain 'D' and resid 377 through 381 removed outlier: 4.179A pdb=" N HIS D 381 " --> pdb=" O ALA D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 399 removed outlier: 4.363A pdb=" N TRP D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP D 393 " --> pdb=" O ILE D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 Processing helix chain 'D' and resid 431 through 452 removed outlier: 3.606A pdb=" N ILE D 435 " --> pdb=" O PRO D 431 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR A 21 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 10 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 54 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 49 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR B 21 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 10 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 54 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 49 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 10 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU C 54 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP C 49 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 17 through 21 removed outlier: 3.712A pdb=" N THR D 21 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 10 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU D 54 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP D 49 " --> pdb=" O GLU D 54 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 2016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.95 Time building geometry restraints manager: 7.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12160 1.03 - 1.23: 36 1.23 - 1.42: 5800 1.42 - 1.61: 7400 1.61 - 1.81: 108 Bond restraints: 25504 Sorted by residual: bond pdb=" O12 POV A 603 " pdb=" P POV A 603 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" O12 POV C 603 " pdb=" P POV C 603 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" O12 POV D 603 " pdb=" P POV D 603 " ideal model delta sigma weight residual 1.657 1.607 0.050 2.00e-02 2.50e+03 6.29e+00 bond pdb=" O12 POV B 603 " pdb=" P POV B 603 " ideal model delta sigma weight residual 1.657 1.607 0.050 2.00e-02 2.50e+03 6.20e+00 bond pdb=" C11 POV A 603 " pdb=" O12 POV A 603 " ideal model delta sigma weight residual 1.408 1.455 -0.047 2.00e-02 2.50e+03 5.49e+00 ... (remaining 25499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 43919 1.25 - 2.49: 1664 2.49 - 3.74: 119 3.74 - 4.99: 34 4.99 - 6.23: 8 Bond angle restraints: 45744 Sorted by residual: angle pdb=" O11 POV A 603 " pdb=" P POV A 603 " pdb=" O12 POV A 603 " ideal model delta sigma weight residual 97.67 103.90 -6.23 3.00e+00 1.11e-01 4.32e+00 angle pdb=" O11 POV C 603 " pdb=" P POV C 603 " pdb=" O12 POV C 603 " ideal model delta sigma weight residual 97.67 103.89 -6.22 3.00e+00 1.11e-01 4.30e+00 angle pdb=" O11 POV B 603 " pdb=" P POV B 603 " pdb=" O12 POV B 603 " ideal model delta sigma weight residual 97.67 103.87 -6.20 3.00e+00 1.11e-01 4.27e+00 angle pdb=" O11 POV D 603 " pdb=" P POV D 603 " pdb=" O12 POV D 603 " ideal model delta sigma weight residual 97.67 103.84 -6.17 3.00e+00 1.11e-01 4.23e+00 angle pdb=" N GLU B 181 " pdb=" CA GLU B 181 " pdb=" CB GLU B 181 " ideal model delta sigma weight residual 113.65 110.94 2.71 1.47e+00 4.63e-01 3.39e+00 ... (remaining 45739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 11211 16.07 - 32.13: 717 32.13 - 48.20: 168 48.20 - 64.27: 88 64.27 - 80.33: 16 Dihedral angle restraints: 12200 sinusoidal: 6400 harmonic: 5800 Sorted by residual: dihedral pdb=" CA ILE A 318 " pdb=" CB ILE A 318 " pdb=" CG1 ILE A 318 " pdb=" CD1 ILE A 318 " ideal model delta sinusoidal sigma weight residual 180.00 133.72 46.28 3 1.50e+01 4.44e-03 8.31e+00 dihedral pdb=" CA ILE D 318 " pdb=" CB ILE D 318 " pdb=" CG1 ILE D 318 " pdb=" CD1 ILE D 318 " ideal model delta sinusoidal sigma weight residual 180.00 133.74 46.26 3 1.50e+01 4.44e-03 8.31e+00 dihedral pdb=" CA ILE B 318 " pdb=" CB ILE B 318 " pdb=" CG1 ILE B 318 " pdb=" CD1 ILE B 318 " ideal model delta sinusoidal sigma weight residual 180.00 133.74 46.26 3 1.50e+01 4.44e-03 8.31e+00 ... (remaining 12197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1135 0.024 - 0.049: 502 0.049 - 0.073: 192 0.073 - 0.097: 90 0.097 - 0.121: 41 Chirality restraints: 1960 Sorted by residual: chirality pdb=" CA ILE D 12 " pdb=" N ILE D 12 " pdb=" C ILE D 12 " pdb=" CB ILE D 12 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA ILE C 12 " pdb=" N ILE C 12 " pdb=" C ILE C 12 " pdb=" CB ILE C 12 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA ILE B 12 " pdb=" N ILE B 12 " pdb=" C ILE B 12 " pdb=" CB ILE B 12 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 1957 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 102 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 103 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 103 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 103 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 102 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO D 103 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 102 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO C 103 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 103 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 103 " -0.020 5.00e-02 4.00e+02 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.36: 8096 2.36 - 3.06: 68417 3.06 - 3.75: 85403 3.75 - 4.45: 132921 4.45 - 5.14: 203943 Nonbonded interactions: 498780 Sorted by model distance: nonbonded pdb=" OD2 ASP A 100 " pdb=" HZ1 LYS D 458 " model vdw 1.667 2.450 nonbonded pdb=" HZ1 LYS A 458 " pdb=" OD2 ASP B 100 " model vdw 1.668 2.450 nonbonded pdb=" HZ1 LYS B 458 " pdb=" OD2 ASP C 100 " model vdw 1.672 2.450 nonbonded pdb=" HZ1 LYS C 458 " pdb=" OD2 ASP D 100 " model vdw 1.673 2.450 nonbonded pdb=" O GLU B 210 " pdb="HD21 ASN B 216 " model vdw 1.693 2.450 ... (remaining 498775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 463 or resid 601 through 603)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.000 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: 0.410 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 64.890 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.040 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:10.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13320 Z= 0.258 Angle : 0.527 6.232 18136 Z= 0.247 Chirality : 0.036 0.121 1960 Planarity : 0.004 0.035 2252 Dihedral : 11.032 80.333 4768 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.61 % Allowed : 3.36 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.22), residues: 1552 helix: 1.68 (0.18), residues: 908 sheet: -2.91 (0.85), residues: 40 loop : -0.95 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 255 HIS 0.001 0.000 HIS A 60 PHE 0.006 0.001 PHE C 328 TYR 0.005 0.001 TYR C 71 ARG 0.003 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 205 time to evaluate : 1.933 Fit side-chains REVERT: A 412 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.7712 (p) REVERT: A 447 MET cc_start: 0.8507 (mmm) cc_final: 0.8121 (mmt) REVERT: B 412 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.7695 (p) REVERT: B 447 MET cc_start: 0.8497 (mmm) cc_final: 0.8107 (mmt) REVERT: C 412 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.7690 (p) REVERT: C 447 MET cc_start: 0.8499 (mmm) cc_final: 0.8109 (mmt) REVERT: D 412 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.7681 (p) REVERT: D 447 MET cc_start: 0.8499 (mmm) cc_final: 0.8112 (mmt) outliers start: 8 outliers final: 0 residues processed: 213 average time/residue: 2.4769 time to fit residues: 580.6470 Evaluate side-chains 145 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13320 Z= 0.350 Angle : 0.580 6.779 18136 Z= 0.301 Chirality : 0.042 0.149 1960 Planarity : 0.005 0.045 2252 Dihedral : 8.822 85.302 1980 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.15 % Allowed : 10.09 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1552 helix: 1.29 (0.17), residues: 932 sheet: -2.44 (0.74), residues: 40 loop : -1.08 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.004 0.001 HIS C 60 PHE 0.016 0.002 PHE A 384 TYR 0.009 0.001 TYR C 48 ARG 0.002 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.8164 (tpp80) cc_final: 0.7694 (ttm-80) REVERT: A 262 MET cc_start: 0.8505 (mmp) cc_final: 0.8108 (mmp) REVERT: A 412 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8477 (p) REVERT: B 23 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7694 (ttm-80) REVERT: B 412 SER cc_start: 0.9090 (OUTLIER) cc_final: 0.8478 (p) REVERT: B 447 MET cc_start: 0.8728 (mmm) cc_final: 0.8327 (mmt) REVERT: C 23 ARG cc_start: 0.8171 (tpp80) cc_final: 0.7690 (ttm-80) REVERT: C 412 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8479 (p) REVERT: D 23 ARG cc_start: 0.8174 (tpp80) cc_final: 0.7690 (ttm-80) REVERT: D 412 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8481 (p) outliers start: 15 outliers final: 10 residues processed: 150 average time/residue: 1.8816 time to fit residues: 318.8671 Evaluate side-chains 135 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 140 optimal weight: 5.9990 chunk 48 optimal weight: 0.0070 chunk 113 optimal weight: 0.0070 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 13320 Z= 0.138 Angle : 0.453 4.691 18136 Z= 0.228 Chirality : 0.037 0.131 1960 Planarity : 0.004 0.037 2252 Dihedral : 8.059 89.987 1980 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.22 % Allowed : 9.56 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.22), residues: 1552 helix: 1.69 (0.17), residues: 948 sheet: -2.24 (0.75), residues: 40 loop : -0.89 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 255 HIS 0.002 0.000 HIS C 383 PHE 0.014 0.001 PHE B 56 TYR 0.005 0.001 TYR B 407 ARG 0.001 0.000 ARG B 368 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 2.015 Fit side-chains REVERT: A 23 ARG cc_start: 0.8191 (tpp80) cc_final: 0.7745 (ttm-80) REVERT: A 262 MET cc_start: 0.8445 (mmp) cc_final: 0.8140 (mmp) REVERT: A 447 MET cc_start: 0.8719 (mmm) cc_final: 0.8383 (mmt) REVERT: B 23 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7737 (ttm-80) REVERT: B 262 MET cc_start: 0.8440 (mmp) cc_final: 0.8130 (mmp) REVERT: B 324 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8083 (mp) REVERT: B 447 MET cc_start: 0.8717 (mmm) cc_final: 0.8377 (mmt) REVERT: C 23 ARG cc_start: 0.8160 (tpp80) cc_final: 0.7717 (ttm-80) REVERT: C 262 MET cc_start: 0.8442 (mmp) cc_final: 0.8129 (mmp) REVERT: C 324 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8082 (mp) REVERT: C 447 MET cc_start: 0.8721 (mmm) cc_final: 0.8384 (mmt) REVERT: D 23 ARG cc_start: 0.8163 (tpp80) cc_final: 0.7721 (ttm-80) REVERT: D 262 MET cc_start: 0.8445 (mmp) cc_final: 0.8126 (mmp) REVERT: D 324 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8083 (mp) REVERT: D 447 MET cc_start: 0.8718 (mmm) cc_final: 0.8385 (mmt) outliers start: 16 outliers final: 4 residues processed: 147 average time/residue: 1.8876 time to fit residues: 313.5962 Evaluate side-chains 130 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 ASN C 276 ASN D 276 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13320 Z= 0.293 Angle : 0.532 5.994 18136 Z= 0.270 Chirality : 0.040 0.131 1960 Planarity : 0.005 0.044 2252 Dihedral : 7.991 76.074 1976 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.92 % Allowed : 10.78 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1552 helix: 1.52 (0.17), residues: 940 sheet: -1.93 (0.76), residues: 40 loop : -1.10 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 392 HIS 0.003 0.001 HIS A 60 PHE 0.015 0.001 PHE B 56 TYR 0.008 0.001 TYR C 365 ARG 0.001 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.927 Fit side-chains REVERT: A 23 ARG cc_start: 0.8225 (tpp80) cc_final: 0.7692 (ttm-80) REVERT: A 262 MET cc_start: 0.8498 (mmp) cc_final: 0.8203 (mmp) REVERT: B 23 ARG cc_start: 0.8227 (tpp80) cc_final: 0.7687 (ttm-80) REVERT: B 262 MET cc_start: 0.8496 (mmp) cc_final: 0.8196 (mmp) REVERT: B 324 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8047 (mp) REVERT: B 447 MET cc_start: 0.8727 (mmm) cc_final: 0.8429 (mmt) REVERT: C 23 ARG cc_start: 0.8228 (tpp80) cc_final: 0.7693 (ttm-80) REVERT: C 262 MET cc_start: 0.8498 (mmp) cc_final: 0.8194 (mmp) REVERT: C 324 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8040 (mp) REVERT: D 23 ARG cc_start: 0.8233 (tpp80) cc_final: 0.7695 (ttm-80) REVERT: D 262 MET cc_start: 0.8503 (mmp) cc_final: 0.8200 (mmp) REVERT: D 324 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8039 (mp) outliers start: 12 outliers final: 8 residues processed: 132 average time/residue: 2.0687 time to fit residues: 305.2133 Evaluate side-chains 133 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 352 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13320 Z= 0.290 Angle : 0.526 5.900 18136 Z= 0.268 Chirality : 0.040 0.130 1960 Planarity : 0.005 0.045 2252 Dihedral : 7.390 53.832 1976 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.84 % Allowed : 10.17 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1552 helix: 1.45 (0.17), residues: 940 sheet: -1.68 (0.77), residues: 40 loop : -1.19 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.003 0.001 HIS D 60 PHE 0.017 0.001 PHE A 56 TYR 0.009 0.001 TYR D 365 ARG 0.001 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 2.738 Fit side-chains REVERT: A 262 MET cc_start: 0.8552 (mmp) cc_final: 0.8271 (mmp) REVERT: B 262 MET cc_start: 0.8552 (mmp) cc_final: 0.8270 (mmp) REVERT: B 324 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8107 (mp) REVERT: C 262 MET cc_start: 0.8550 (mmp) cc_final: 0.8268 (mmp) REVERT: C 324 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8079 (mp) REVERT: D 262 MET cc_start: 0.8549 (mmp) cc_final: 0.8264 (mmp) REVERT: D 324 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8076 (mp) outliers start: 11 outliers final: 8 residues processed: 132 average time/residue: 2.1598 time to fit residues: 318.4454 Evaluate side-chains 131 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 352 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13320 Z= 0.258 Angle : 0.520 5.579 18136 Z= 0.264 Chirality : 0.039 0.126 1960 Planarity : 0.005 0.044 2252 Dihedral : 6.836 53.444 1976 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.15 % Allowed : 11.31 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1552 helix: 1.52 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -1.11 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.002 0.001 HIS A 60 PHE 0.018 0.001 PHE C 56 TYR 0.008 0.001 TYR B 365 ARG 0.001 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.976 Fit side-chains REVERT: A 262 MET cc_start: 0.8550 (mmp) cc_final: 0.8283 (mmp) REVERT: A 412 SER cc_start: 0.9093 (OUTLIER) cc_final: 0.8444 (p) REVERT: A 447 MET cc_start: 0.8725 (mmm) cc_final: 0.8501 (mmt) REVERT: B 262 MET cc_start: 0.8546 (mmp) cc_final: 0.8283 (mmp) REVERT: B 324 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8110 (mp) REVERT: B 412 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8444 (p) REVERT: C 262 MET cc_start: 0.8544 (mmp) cc_final: 0.8283 (mmp) REVERT: C 324 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8098 (mp) REVERT: C 412 SER cc_start: 0.9097 (OUTLIER) cc_final: 0.8447 (p) REVERT: C 447 MET cc_start: 0.8723 (mmm) cc_final: 0.8502 (mmt) REVERT: D 262 MET cc_start: 0.8543 (mmp) cc_final: 0.8280 (mmp) REVERT: D 324 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8094 (mp) REVERT: D 412 SER cc_start: 0.9097 (OUTLIER) cc_final: 0.8448 (p) REVERT: D 447 MET cc_start: 0.8726 (mmm) cc_final: 0.8503 (mmt) outliers start: 15 outliers final: 8 residues processed: 140 average time/residue: 2.0035 time to fit residues: 314.3932 Evaluate side-chains 143 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13320 Z= 0.241 Angle : 0.507 5.382 18136 Z= 0.257 Chirality : 0.039 0.129 1960 Planarity : 0.005 0.044 2252 Dihedral : 6.675 52.929 1976 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.15 % Allowed : 11.24 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1552 helix: 1.57 (0.17), residues: 940 sheet: -0.79 (0.88), residues: 40 loop : -1.13 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.003 0.000 HIS C 60 PHE 0.015 0.001 PHE B 384 TYR 0.007 0.001 TYR C 365 ARG 0.001 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.980 Fit side-chains REVERT: A 262 MET cc_start: 0.8556 (mmp) cc_final: 0.8311 (mmp) REVERT: A 412 SER cc_start: 0.9084 (OUTLIER) cc_final: 0.8429 (p) REVERT: B 262 MET cc_start: 0.8554 (mmp) cc_final: 0.8312 (mmp) REVERT: B 324 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8121 (mp) REVERT: B 412 SER cc_start: 0.9086 (OUTLIER) cc_final: 0.8429 (p) REVERT: B 447 MET cc_start: 0.8745 (mmm) cc_final: 0.8489 (mmt) REVERT: C 262 MET cc_start: 0.8554 (mmp) cc_final: 0.8311 (mmp) REVERT: C 324 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8122 (mp) REVERT: C 412 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8430 (p) REVERT: D 262 MET cc_start: 0.8553 (mmp) cc_final: 0.8308 (mmp) REVERT: D 324 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8119 (mp) REVERT: D 412 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8431 (p) outliers start: 15 outliers final: 8 residues processed: 137 average time/residue: 2.0189 time to fit residues: 310.1169 Evaluate side-chains 141 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 136 optimal weight: 0.1980 chunk 144 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13320 Z= 0.171 Angle : 0.476 4.533 18136 Z= 0.239 Chirality : 0.038 0.124 1960 Planarity : 0.005 0.042 2252 Dihedral : 6.383 49.997 1976 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.84 % Allowed : 11.70 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1552 helix: 1.64 (0.17), residues: 956 sheet: -0.58 (0.92), residues: 40 loop : -0.91 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.002 0.000 HIS D 60 PHE 0.012 0.001 PHE A 384 TYR 0.006 0.001 TYR A 365 ARG 0.001 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 2.052 Fit side-chains REVERT: B 324 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8090 (mp) REVERT: B 447 MET cc_start: 0.8727 (mmm) cc_final: 0.8481 (mmt) REVERT: C 324 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8102 (mp) REVERT: D 324 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8102 (mp) outliers start: 11 outliers final: 8 residues processed: 136 average time/residue: 2.0515 time to fit residues: 313.3382 Evaluate side-chains 139 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 352 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 chunk 84 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13320 Z= 0.230 Angle : 0.505 5.209 18136 Z= 0.254 Chirality : 0.038 0.125 1960 Planarity : 0.005 0.043 2252 Dihedral : 6.608 51.914 1976 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.84 % Allowed : 12.84 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.22), residues: 1552 helix: 1.68 (0.18), residues: 940 sheet: -0.45 (0.94), residues: 40 loop : -1.04 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 392 HIS 0.002 0.000 HIS D 60 PHE 0.015 0.001 PHE A 384 TYR 0.007 0.001 TYR B 365 ARG 0.001 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.797 Fit side-chains REVERT: B 324 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8101 (mp) REVERT: B 447 MET cc_start: 0.8720 (mmm) cc_final: 0.8458 (mmt) REVERT: C 324 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8098 (mp) REVERT: D 324 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8098 (mp) outliers start: 11 outliers final: 8 residues processed: 147 average time/residue: 1.8119 time to fit residues: 298.2987 Evaluate side-chains 144 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13320 Z= 0.176 Angle : 0.482 4.434 18136 Z= 0.241 Chirality : 0.038 0.122 1960 Planarity : 0.005 0.042 2252 Dihedral : 6.406 49.402 1976 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.38 % Allowed : 12.69 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.22), residues: 1552 helix: 1.70 (0.17), residues: 956 sheet: -0.32 (0.95), residues: 40 loop : -0.88 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.003 0.000 HIS A 60 PHE 0.013 0.001 PHE C 93 TYR 0.006 0.001 TYR B 191 ARG 0.001 0.000 ARG B 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Residue TYR 235 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue THR 397 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue LYS 456 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.974 Fit side-chains REVERT: A 412 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8408 (p) REVERT: B 324 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8074 (mp) REVERT: B 412 SER cc_start: 0.9065 (OUTLIER) cc_final: 0.8377 (p) REVERT: B 447 MET cc_start: 0.8717 (mmm) cc_final: 0.8470 (mmt) REVERT: C 324 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8071 (mp) REVERT: C 412 SER cc_start: 0.9067 (OUTLIER) cc_final: 0.8406 (p) REVERT: D 324 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8071 (mp) REVERT: D 412 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8407 (p) outliers start: 18 outliers final: 8 residues processed: 152 average time/residue: 1.9951 time to fit residues: 340.3970 Evaluate side-chains 150 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 127 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.184757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3572 r_free = 0.3572 target = 0.136862 restraints weight = 37353.618| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.37 r_work: 0.3319 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13320 Z= 0.215 Angle : 0.500 4.941 18136 Z= 0.251 Chirality : 0.038 0.123 1960 Planarity : 0.005 0.042 2252 Dihedral : 6.542 50.822 1976 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.15 % Allowed : 13.76 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.22), residues: 1552 helix: 1.73 (0.17), residues: 940 sheet: -0.27 (0.95), residues: 40 loop : -1.00 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 392 HIS 0.002 0.000 HIS A 60 PHE 0.014 0.001 PHE C 384 TYR 0.006 0.001 TYR B 365 ARG 0.001 0.000 ARG A 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6908.98 seconds wall clock time: 121 minutes 43.19 seconds (7303.19 seconds total)