Starting phenix.real_space_refine on Wed Mar 4 17:53:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v0g_20997/03_2026/6v0g_20997.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v0g_20997/03_2026/6v0g_20997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v0g_20997/03_2026/6v0g_20997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v0g_20997/03_2026/6v0g_20997.map" model { file = "/net/cci-nas-00/data/ceres_data/6v0g_20997/03_2026/6v0g_20997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v0g_20997/03_2026/6v0g_20997.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 9642 2.51 5 N 2580 2.21 5 O 2988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15252 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.18, per 1000 atoms: 0.14 Number of scatterers: 15252 At special positions: 0 Unit cell: (113.97, 113.97, 103.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2988 8.00 N 2580 7.00 C 9642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 611.9 milliseconds 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 30 sheets defined 15.2% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 83 through 86 removed outlier: 3.644A pdb=" N ARG A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 209 through 214 removed outlier: 4.333A pdb=" N ASP A 213 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.918A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.673A pdb=" N GLN A 278 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 removed outlier: 4.174A pdb=" N THR A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 removed outlier: 4.197A pdb=" N LEU A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 86 removed outlier: 3.644A pdb=" N ARG B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 86' Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 116 through 122 Processing helix chain 'B' and resid 209 through 214 removed outlier: 4.333A pdb=" N ASP B 213 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.918A pdb=" N VAL B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.672A pdb=" N GLN B 278 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 333 removed outlier: 4.174A pdb=" N THR B 333 " --> pdb=" O PRO B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 removed outlier: 4.197A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 86 removed outlier: 3.644A pdb=" N ARG C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 86' Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 116 through 122 Processing helix chain 'C' and resid 209 through 214 removed outlier: 4.332A pdb=" N ASP C 213 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.918A pdb=" N VAL C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 removed outlier: 3.673A pdb=" N GLN C 278 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 333 removed outlier: 4.173A pdb=" N THR C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 removed outlier: 4.197A pdb=" N LEU C 358 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 86 removed outlier: 3.644A pdb=" N ARG D 86 " --> pdb=" O ASP D 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 83 through 86' Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 116 through 122 Processing helix chain 'D' and resid 209 through 214 removed outlier: 4.332A pdb=" N ASP D 213 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.918A pdb=" N VAL D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 removed outlier: 3.673A pdb=" N GLN D 278 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 333 removed outlier: 4.173A pdb=" N THR D 333 " --> pdb=" O PRO D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 removed outlier: 4.197A pdb=" N LEU D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 86 removed outlier: 3.644A pdb=" N ARG E 86 " --> pdb=" O ASP E 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 83 through 86' Processing helix chain 'E' and resid 95 through 102 Processing helix chain 'E' and resid 116 through 122 Processing helix chain 'E' and resid 209 through 214 removed outlier: 4.333A pdb=" N ASP E 213 " --> pdb=" O ARG E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 248 removed outlier: 3.918A pdb=" N VAL E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 278 removed outlier: 3.672A pdb=" N GLN E 278 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 333 removed outlier: 4.173A pdb=" N THR E 333 " --> pdb=" O PRO E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 361 removed outlier: 4.197A pdb=" N LEU E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 86 removed outlier: 3.644A pdb=" N ARG F 86 " --> pdb=" O ASP F 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 83 through 86' Processing helix chain 'F' and resid 95 through 102 Processing helix chain 'F' and resid 116 through 122 Processing helix chain 'F' and resid 209 through 214 removed outlier: 4.333A pdb=" N ASP F 213 " --> pdb=" O ARG F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 248 removed outlier: 3.918A pdb=" N VAL F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.672A pdb=" N GLN F 278 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 removed outlier: 4.173A pdb=" N THR F 333 " --> pdb=" O PRO F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 361 removed outlier: 4.198A pdb=" N LEU F 358 " --> pdb=" O ASN F 354 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.159A pdb=" N VAL A 66 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS A 91 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE A 79 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU A 81 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYS A 87 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR A 50 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 167 removed outlier: 6.855A pdb=" N VAL A 202 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR A 192 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP A 204 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 179 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE A 221 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 230 through 231 removed outlier: 3.527A pdb=" N ALA B 236 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 236 through 237 removed outlier: 3.526A pdb=" N ALA A 236 " --> pdb=" O VAL F 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.358A pdb=" N LEU A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU A 324 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU A 313 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A 322 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU A 315 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LYS A 320 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LYS A 284 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.158A pdb=" N VAL B 66 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS B 91 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 79 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU B 89 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU B 81 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS B 87 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR B 50 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 107 through 111 Processing sheet with id=AA9, first strand: chain 'B' and resid 161 through 167 removed outlier: 6.855A pdb=" N VAL B 202 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR B 192 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP B 204 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 179 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 230 through 231 removed outlier: 3.526A pdb=" N ALA C 236 " --> pdb=" O VAL B 231 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 340 through 344 removed outlier: 6.358A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU B 324 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 313 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR B 322 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU B 315 " --> pdb=" O LYS B 320 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LYS B 320 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.158A pdb=" N VAL C 66 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS C 91 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE C 79 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU C 89 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU C 81 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYS C 87 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR C 50 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 107 through 111 Processing sheet with id=AB5, first strand: chain 'C' and resid 161 through 167 removed outlier: 6.855A pdb=" N VAL C 202 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR C 192 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASP C 204 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 230 through 231 removed outlier: 3.526A pdb=" N ALA D 236 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 340 through 344 removed outlier: 6.358A pdb=" N LEU C 300 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU C 324 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU C 313 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR C 322 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU C 315 " --> pdb=" O LYS C 320 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LYS C 320 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.159A pdb=" N VAL D 66 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS D 91 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE D 79 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU D 89 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU D 81 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYS D 87 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR D 50 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 107 through 111 Processing sheet with id=AC1, first strand: chain 'D' and resid 161 through 167 removed outlier: 6.855A pdb=" N VAL D 202 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR D 192 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP D 204 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL D 179 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 230 through 231 removed outlier: 3.505A pdb=" N ALA E 236 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.359A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU D 324 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU D 313 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR D 322 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU D 315 " --> pdb=" O LYS D 320 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LYS D 320 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.159A pdb=" N VAL E 66 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LYS E 91 " --> pdb=" O GLN E 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE E 79 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU E 89 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU E 81 " --> pdb=" O LYS E 87 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYS E 87 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR E 50 " --> pdb=" O PHE E 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 107 through 111 Processing sheet with id=AC6, first strand: chain 'E' and resid 161 through 167 removed outlier: 6.855A pdb=" N VAL E 202 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR E 192 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP E 204 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL E 179 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 230 through 231 removed outlier: 3.528A pdb=" N ALA F 236 " --> pdb=" O VAL E 231 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.359A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU E 324 " --> pdb=" O THR E 311 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 313 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR E 322 " --> pdb=" O LEU E 313 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU E 315 " --> pdb=" O LYS E 320 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LYS E 320 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 65 through 68 removed outlier: 6.159A pdb=" N VAL F 66 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS F 91 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE F 79 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU F 89 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU F 81 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS F 87 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR F 50 " --> pdb=" O PHE F 145 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 107 through 111 Processing sheet with id=AD2, first strand: chain 'F' and resid 161 through 167 removed outlier: 6.855A pdb=" N VAL F 202 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR F 192 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP F 204 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL F 179 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE F 221 " --> pdb=" O TYR F 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 340 through 344 removed outlier: 6.358A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU F 324 " --> pdb=" O THR F 311 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU F 313 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR F 322 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU F 315 " --> pdb=" O LYS F 320 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LYS F 320 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1152 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: 1.92 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4932 1.34 - 1.45: 2018 1.45 - 1.57: 8464 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 15498 Sorted by residual: bond pdb=" CB VAL F 201 " pdb=" CG2 VAL F 201 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.80e+00 bond pdb=" CB VAL C 201 " pdb=" CG2 VAL C 201 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.80e+00 bond pdb=" CB VAL D 201 " pdb=" CG2 VAL D 201 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.80e+00 bond pdb=" CB VAL A 201 " pdb=" CG2 VAL A 201 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.78e+00 bond pdb=" CB VAL B 201 " pdb=" CG2 VAL B 201 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 ... (remaining 15493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 20862 4.60 - 9.21: 120 9.21 - 13.81: 6 13.81 - 18.42: 6 18.42 - 23.02: 6 Bond angle restraints: 21000 Sorted by residual: angle pdb=" CA LEU A 240 " pdb=" CB LEU A 240 " pdb=" CG LEU A 240 " ideal model delta sigma weight residual 116.30 102.04 14.26 3.50e+00 8.16e-02 1.66e+01 angle pdb=" CA LEU C 240 " pdb=" CB LEU C 240 " pdb=" CG LEU C 240 " ideal model delta sigma weight residual 116.30 102.06 14.24 3.50e+00 8.16e-02 1.65e+01 angle pdb=" CA LEU F 240 " pdb=" CB LEU F 240 " pdb=" CG LEU F 240 " ideal model delta sigma weight residual 116.30 102.07 14.23 3.50e+00 8.16e-02 1.65e+01 angle pdb=" CA LEU B 240 " pdb=" CB LEU B 240 " pdb=" CG LEU B 240 " ideal model delta sigma weight residual 116.30 102.12 14.18 3.50e+00 8.16e-02 1.64e+01 angle pdb=" CA LEU E 240 " pdb=" CB LEU E 240 " pdb=" CG LEU E 240 " ideal model delta sigma weight residual 116.30 102.12 14.18 3.50e+00 8.16e-02 1.64e+01 ... (remaining 20995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.15: 8893 15.15 - 30.30: 387 30.30 - 45.46: 110 45.46 - 60.61: 12 60.61 - 75.76: 30 Dihedral angle restraints: 9432 sinusoidal: 3756 harmonic: 5676 Sorted by residual: dihedral pdb=" CA PRO C 317 " pdb=" C PRO C 317 " pdb=" N GLY C 318 " pdb=" CA GLY C 318 " ideal model delta harmonic sigma weight residual -180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA PRO F 317 " pdb=" C PRO F 317 " pdb=" N GLY F 318 " pdb=" CA GLY F 318 " ideal model delta harmonic sigma weight residual -180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA PRO E 317 " pdb=" C PRO E 317 " pdb=" N GLY E 318 " pdb=" CA GLY E 318 " ideal model delta harmonic sigma weight residual 180.00 -156.20 -23.80 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 9429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2086 0.091 - 0.183: 337 0.183 - 0.274: 19 0.274 - 0.365: 0 0.365 - 0.457: 6 Chirality restraints: 2448 Sorted by residual: chirality pdb=" CG LEU B 240 " pdb=" CB LEU B 240 " pdb=" CD1 LEU B 240 " pdb=" CD2 LEU B 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" CG LEU E 240 " pdb=" CB LEU E 240 " pdb=" CD1 LEU E 240 " pdb=" CD2 LEU E 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.18e+00 chirality pdb=" CG LEU A 240 " pdb=" CB LEU A 240 " pdb=" CD1 LEU A 240 " pdb=" CD2 LEU A 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.45 2.00e-01 2.50e+01 5.17e+00 ... (remaining 2445 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 105 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C GLU C 105 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU C 105 " 0.016 2.00e-02 2.50e+03 pdb=" N THR C 106 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 105 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C GLU F 105 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU F 105 " 0.016 2.00e-02 2.50e+03 pdb=" N THR F 106 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 105 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C GLU A 105 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU A 105 " 0.016 2.00e-02 2.50e+03 pdb=" N THR A 106 " 0.014 2.00e-02 2.50e+03 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3966 2.81 - 3.33: 12905 3.33 - 3.86: 24340 3.86 - 4.38: 27441 4.38 - 4.90: 48134 Nonbonded interactions: 116786 Sorted by model distance: nonbonded pdb=" O ARG B 103 " pdb=" OG1 THR B 106 " model vdw 2.289 3.040 nonbonded pdb=" O ARG E 103 " pdb=" OG1 THR E 106 " model vdw 2.289 3.040 nonbonded pdb=" O ARG D 103 " pdb=" OG1 THR D 106 " model vdw 2.289 3.040 nonbonded pdb=" O ARG F 103 " pdb=" OG1 THR F 106 " model vdw 2.289 3.040 nonbonded pdb=" O ARG C 103 " pdb=" OG1 THR C 106 " model vdw 2.290 3.040 ... (remaining 116781 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.240 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.008 0.072 15498 Z= 0.351 Angle : 1.162 23.020 21000 Z= 0.594 Chirality : 0.067 0.457 2448 Planarity : 0.008 0.058 2736 Dihedral : 11.009 75.760 5808 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.15), residues: 1998 helix: -3.43 (0.21), residues: 192 sheet: -1.13 (0.20), residues: 570 loop : -2.18 (0.14), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 374 TYR 0.018 0.003 TYR D 68 PHE 0.042 0.005 PHE C 221 TRP 0.008 0.002 TRP F 109 HIS 0.005 0.002 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00821 (15498) covalent geometry : angle 1.16175 (21000) hydrogen bonds : bond 0.19338 ( 468) hydrogen bonds : angle 10.73482 ( 1152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8013 (tt) cc_final: 0.7784 (tp) REVERT: A 190 TYR cc_start: 0.8795 (t80) cc_final: 0.8391 (t80) REVERT: A 314 ASP cc_start: 0.7563 (m-30) cc_final: 0.7362 (m-30) REVERT: B 134 MET cc_start: 0.7804 (ptm) cc_final: 0.7529 (ptp) REVERT: C 54 MET cc_start: 0.6364 (mtp) cc_final: 0.5779 (mmm) REVERT: C 87 LYS cc_start: 0.7115 (ttmp) cc_final: 0.6621 (tppt) REVERT: C 110 LEU cc_start: 0.9012 (tp) cc_final: 0.8777 (tp) REVERT: C 114 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8558 (mttm) REVERT: C 144 HIS cc_start: 0.7732 (t-90) cc_final: 0.7384 (t70) REVERT: C 190 TYR cc_start: 0.8867 (t80) cc_final: 0.8500 (t80) REVERT: D 107 GLN cc_start: 0.7595 (mt0) cc_final: 0.7304 (mm110) REVERT: D 117 LEU cc_start: 0.7908 (tt) cc_final: 0.7688 (tp) REVERT: D 190 TYR cc_start: 0.8796 (t80) cc_final: 0.8386 (t80) REVERT: E 134 MET cc_start: 0.7790 (ptm) cc_final: 0.7553 (ptp) REVERT: F 87 LYS cc_start: 0.7213 (ttmp) cc_final: 0.6761 (tppt) REVERT: F 110 LEU cc_start: 0.9011 (tp) cc_final: 0.8771 (tp) REVERT: F 114 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8582 (mttm) REVERT: F 144 HIS cc_start: 0.7680 (t-90) cc_final: 0.7395 (t70) REVERT: F 190 TYR cc_start: 0.8846 (t80) cc_final: 0.8481 (t80) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.1229 time to fit residues: 72.1603 Evaluate side-chains 233 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 HIS A 316 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS D 316 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 ASN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115550 restraints weight = 22482.578| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.66 r_work: 0.3253 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15498 Z= 0.136 Angle : 0.682 17.224 21000 Z= 0.333 Chirality : 0.047 0.191 2448 Planarity : 0.005 0.045 2736 Dihedral : 5.157 17.353 2136 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.79 % Allowed : 9.49 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.16), residues: 1998 helix: -2.56 (0.28), residues: 198 sheet: -0.86 (0.18), residues: 696 loop : -1.87 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 155 TYR 0.009 0.001 TYR F 154 PHE 0.014 0.002 PHE A 253 TRP 0.007 0.001 TRP E 222 HIS 0.002 0.001 HIS E 164 Details of bonding type rmsd covalent geometry : bond 0.00291 (15498) covalent geometry : angle 0.68207 (21000) hydrogen bonds : bond 0.04264 ( 468) hydrogen bonds : angle 7.40634 ( 1152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 255 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 107 GLN cc_start: 0.8281 (mm110) cc_final: 0.7786 (mt0) REVERT: A 109 TRP cc_start: 0.8423 (p90) cc_final: 0.8077 (p90) REVERT: A 117 LEU cc_start: 0.8066 (tt) cc_final: 0.7866 (tp) REVERT: A 135 MET cc_start: 0.7187 (mtt) cc_final: 0.6931 (tpp) REVERT: B 69 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8232 (mt0) REVERT: B 98 MET cc_start: 0.7986 (tpp) cc_final: 0.7537 (tpp) REVERT: B 135 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6777 (tpp) REVERT: B 142 GLN cc_start: 0.4962 (tt0) cc_final: 0.4596 (tt0) REVERT: C 54 MET cc_start: 0.6247 (mtp) cc_final: 0.5991 (mmm) REVERT: C 68 TYR cc_start: 0.8647 (t80) cc_final: 0.8395 (t80) REVERT: C 114 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8420 (mttm) REVERT: C 166 GLN cc_start: 0.8061 (mt0) cc_final: 0.7361 (mp10) REVERT: C 190 TYR cc_start: 0.8957 (t80) cc_final: 0.8553 (t80) REVERT: D 224 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8225 (m) REVERT: E 135 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6861 (tpp) REVERT: F 68 TYR cc_start: 0.8650 (t80) cc_final: 0.8392 (t80) REVERT: F 114 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8339 (mttm) REVERT: F 166 GLN cc_start: 0.8100 (mt0) cc_final: 0.7423 (mp10) REVERT: F 190 TYR cc_start: 0.8970 (t80) cc_final: 0.8589 (t80) outliers start: 47 outliers final: 21 residues processed: 295 average time/residue: 0.1271 time to fit residues: 53.9633 Evaluate side-chains 238 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 242 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 125 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN D 338 ASN E 69 GLN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.111021 restraints weight = 22902.866| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.73 r_work: 0.3169 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15498 Z= 0.233 Angle : 0.712 12.731 21000 Z= 0.355 Chirality : 0.049 0.180 2448 Planarity : 0.005 0.033 2736 Dihedral : 5.288 21.525 2136 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.26 % Allowed : 10.20 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.17), residues: 1998 helix: -1.64 (0.34), residues: 198 sheet: -0.57 (0.19), residues: 672 loop : -1.61 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 220 TYR 0.009 0.002 TYR F 190 PHE 0.020 0.003 PHE F 364 TRP 0.008 0.002 TRP D 222 HIS 0.006 0.001 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00541 (15498) covalent geometry : angle 0.71170 (21000) hydrogen bonds : bond 0.04359 ( 468) hydrogen bonds : angle 7.13367 ( 1152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 0.444 Fit side-chains REVERT: A 107 GLN cc_start: 0.8432 (mm110) cc_final: 0.7904 (mt0) REVERT: B 69 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8062 (mt0) REVERT: B 98 MET cc_start: 0.8243 (tpp) cc_final: 0.7763 (tpp) REVERT: B 135 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7287 (tpp) REVERT: B 142 GLN cc_start: 0.5516 (tt0) cc_final: 0.5262 (tt0) REVERT: C 114 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8455 (mttm) REVERT: C 144 HIS cc_start: 0.7971 (t-90) cc_final: 0.7467 (t-90) REVERT: C 166 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: C 190 TYR cc_start: 0.8976 (t80) cc_final: 0.8582 (t80) REVERT: F 114 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8450 (mttm) REVERT: F 144 HIS cc_start: 0.7974 (t-90) cc_final: 0.7495 (t-90) REVERT: F 166 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: F 190 TYR cc_start: 0.8991 (t80) cc_final: 0.8617 (t80) outliers start: 55 outliers final: 45 residues processed: 273 average time/residue: 0.1208 time to fit residues: 48.9132 Evaluate side-chains 248 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 367 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 167 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.110558 restraints weight = 22842.043| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.56 r_work: 0.3172 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15498 Z= 0.162 Angle : 0.625 12.131 21000 Z= 0.312 Chirality : 0.047 0.181 2448 Planarity : 0.004 0.033 2736 Dihedral : 4.910 19.548 2136 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.68 % Allowed : 10.56 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.18), residues: 1998 helix: -1.26 (0.36), residues: 198 sheet: -0.45 (0.18), residues: 702 loop : -1.52 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 155 TYR 0.017 0.002 TYR D 131 PHE 0.014 0.002 PHE A 253 TRP 0.007 0.002 TRP F 222 HIS 0.004 0.001 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00372 (15498) covalent geometry : angle 0.62499 (21000) hydrogen bonds : bond 0.03815 ( 468) hydrogen bonds : angle 6.79320 ( 1152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 107 GLN cc_start: 0.8385 (mm110) cc_final: 0.7744 (mt0) REVERT: A 324 GLU cc_start: 0.8806 (pt0) cc_final: 0.8600 (pt0) REVERT: B 69 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8200 (mt0) REVERT: B 142 GLN cc_start: 0.5443 (tt0) cc_final: 0.5105 (tt0) REVERT: C 54 MET cc_start: 0.5989 (mmm) cc_final: 0.5669 (tpp) REVERT: C 105 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7438 (tm-30) REVERT: C 114 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8446 (mttm) REVERT: C 190 TYR cc_start: 0.9024 (t80) cc_final: 0.8658 (t80) REVERT: C 191 ASP cc_start: 0.8258 (t70) cc_final: 0.8008 (t0) REVERT: D 224 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8434 (m) REVERT: F 114 LYS cc_start: 0.8942 (mtmt) cc_final: 0.8454 (mttm) REVERT: F 190 TYR cc_start: 0.9025 (t80) cc_final: 0.8665 (t80) REVERT: F 191 ASP cc_start: 0.8229 (t70) cc_final: 0.7974 (t0) outliers start: 62 outliers final: 51 residues processed: 254 average time/residue: 0.1199 time to fit residues: 45.0415 Evaluate side-chains 247 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 195 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 367 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 53 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 107 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS C 166 GLN D 47 ASN D 130 ASN D 338 ASN E 47 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 HIS F 166 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.138112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107173 restraints weight = 23200.637| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.65 r_work: 0.3111 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 15498 Z= 0.303 Angle : 0.746 14.415 21000 Z= 0.372 Chirality : 0.051 0.185 2448 Planarity : 0.005 0.034 2736 Dihedral : 5.549 23.499 2136 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.39 % Allowed : 11.57 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.18), residues: 1998 helix: -1.82 (0.32), residues: 234 sheet: -0.52 (0.19), residues: 636 loop : -1.72 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 220 TYR 0.016 0.002 TYR A 131 PHE 0.020 0.003 PHE A 253 TRP 0.010 0.002 TRP B 222 HIS 0.003 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00716 (15498) covalent geometry : angle 0.74628 (21000) hydrogen bonds : bond 0.04320 ( 468) hydrogen bonds : angle 7.00858 ( 1152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 214 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 107 GLN cc_start: 0.8528 (mm110) cc_final: 0.7822 (mt0) REVERT: B 68 TYR cc_start: 0.8602 (t80) cc_final: 0.7978 (t80) REVERT: B 69 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8451 (mt0) REVERT: C 105 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7594 (tm-30) REVERT: C 114 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8456 (mttm) REVERT: C 124 ASP cc_start: 0.8249 (t0) cc_final: 0.7898 (t0) REVERT: C 190 TYR cc_start: 0.9066 (t80) cc_final: 0.8696 (t80) REVERT: D 190 TYR cc_start: 0.8963 (t80) cc_final: 0.8692 (t80) REVERT: E 105 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: F 105 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7737 (tm-30) REVERT: F 114 LYS cc_start: 0.8964 (mtmt) cc_final: 0.8457 (mttm) REVERT: F 190 TYR cc_start: 0.9131 (t80) cc_final: 0.8820 (t80) outliers start: 74 outliers final: 61 residues processed: 273 average time/residue: 0.1120 time to fit residues: 45.9536 Evaluate side-chains 257 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 195 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 367 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 169 optimal weight: 0.1980 chunk 175 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS D 338 ASN E 69 GLN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 ASN F 107 GLN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 HIS F 166 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.141150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110371 restraints weight = 22690.779| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.53 r_work: 0.3174 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15498 Z= 0.140 Angle : 0.609 11.541 21000 Z= 0.305 Chirality : 0.046 0.166 2448 Planarity : 0.004 0.035 2736 Dihedral : 4.891 20.974 2136 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.15 % Allowed : 12.34 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.18), residues: 1998 helix: -0.98 (0.38), residues: 198 sheet: -0.57 (0.19), residues: 708 loop : -1.36 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 155 TYR 0.015 0.002 TYR A 131 PHE 0.013 0.001 PHE A 253 TRP 0.007 0.001 TRP A 222 HIS 0.002 0.000 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00321 (15498) covalent geometry : angle 0.60928 (21000) hydrogen bonds : bond 0.03649 ( 468) hydrogen bonds : angle 6.66386 ( 1152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 202 time to evaluate : 0.596 Fit side-chains REVERT: A 142 GLN cc_start: 0.5435 (tt0) cc_final: 0.5103 (tt0) REVERT: B 68 TYR cc_start: 0.8096 (t80) cc_final: 0.7437 (t80) REVERT: B 204 ASP cc_start: 0.8197 (p0) cc_final: 0.7862 (p0) REVERT: C 105 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7590 (tm-30) REVERT: C 114 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8434 (mttm) REVERT: C 190 TYR cc_start: 0.8987 (t80) cc_final: 0.8655 (t80) REVERT: C 191 ASP cc_start: 0.8172 (t70) cc_final: 0.7880 (t0) REVERT: E 105 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: E 204 ASP cc_start: 0.8197 (p0) cc_final: 0.7863 (p0) REVERT: F 105 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7652 (tm-30) REVERT: F 114 LYS cc_start: 0.8921 (mtmt) cc_final: 0.8425 (mttm) REVERT: F 190 TYR cc_start: 0.9000 (t80) cc_final: 0.8694 (t80) REVERT: F 191 ASP cc_start: 0.8271 (t70) cc_final: 0.7954 (t0) outliers start: 70 outliers final: 58 residues processed: 254 average time/residue: 0.1123 time to fit residues: 43.2257 Evaluate side-chains 254 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 195 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 367 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 126 optimal weight: 0.0000 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 142 optimal weight: 0.0980 chunk 87 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 GLN C 144 HIS D 144 HIS D 338 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 HIS ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.143344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112109 restraints weight = 22689.767| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.68 r_work: 0.3186 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15498 Z= 0.116 Angle : 0.575 11.227 21000 Z= 0.290 Chirality : 0.045 0.159 2448 Planarity : 0.004 0.035 2736 Dihedral : 4.558 17.886 2136 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.80 % Allowed : 13.40 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.18), residues: 1998 helix: -1.10 (0.38), residues: 210 sheet: -0.46 (0.19), residues: 702 loop : -1.44 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 155 TYR 0.033 0.002 TYR A 68 PHE 0.013 0.001 PHE F 253 TRP 0.007 0.001 TRP C 222 HIS 0.002 0.000 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00262 (15498) covalent geometry : angle 0.57541 (21000) hydrogen bonds : bond 0.03394 ( 468) hydrogen bonds : angle 6.48953 ( 1152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 0.555 Fit side-chains REVERT: A 107 GLN cc_start: 0.8479 (mm110) cc_final: 0.7832 (mt0) REVERT: A 144 HIS cc_start: 0.7425 (t70) cc_final: 0.6054 (m-70) REVERT: A 191 ASP cc_start: 0.8051 (t70) cc_final: 0.7637 (t0) REVERT: B 68 TYR cc_start: 0.7873 (t80) cc_final: 0.7273 (t80) REVERT: B 144 HIS cc_start: 0.7830 (t-170) cc_final: 0.6415 (m-70) REVERT: B 204 ASP cc_start: 0.7974 (p0) cc_final: 0.7603 (p0) REVERT: C 105 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7410 (tm-30) REVERT: C 114 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8386 (mttm) REVERT: C 190 TYR cc_start: 0.8850 (t80) cc_final: 0.8532 (t80) REVERT: C 191 ASP cc_start: 0.7914 (t70) cc_final: 0.7668 (t0) REVERT: C 328 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7413 (t0) REVERT: D 144 HIS cc_start: 0.7413 (t70) cc_final: 0.6026 (m-70) REVERT: D 191 ASP cc_start: 0.8106 (t70) cc_final: 0.7685 (t0) REVERT: E 144 HIS cc_start: 0.7724 (t-170) cc_final: 0.6350 (m-70) REVERT: E 204 ASP cc_start: 0.7974 (p0) cc_final: 0.7607 (p0) REVERT: F 105 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7415 (tm-30) REVERT: F 114 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8378 (mttm) REVERT: F 190 TYR cc_start: 0.8863 (t80) cc_final: 0.8551 (t80) REVERT: F 191 ASP cc_start: 0.7919 (t70) cc_final: 0.7700 (t0) REVERT: F 328 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7404 (t0) outliers start: 64 outliers final: 55 residues processed: 250 average time/residue: 0.1121 time to fit residues: 41.9638 Evaluate side-chains 243 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 186 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 138 LYS Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 367 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 136 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 67 optimal weight: 0.4980 chunk 97 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112004 restraints weight = 22981.347| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.74 r_work: 0.3177 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15498 Z= 0.134 Angle : 0.596 11.595 21000 Z= 0.300 Chirality : 0.045 0.169 2448 Planarity : 0.004 0.035 2736 Dihedral : 4.540 17.283 2136 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.91 % Allowed : 13.70 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.18), residues: 1998 helix: -1.09 (0.37), residues: 210 sheet: -0.22 (0.20), residues: 642 loop : -1.57 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 155 TYR 0.023 0.002 TYR A 68 PHE 0.013 0.001 PHE A 253 TRP 0.014 0.002 TRP D 109 HIS 0.002 0.000 HIS E 144 Details of bonding type rmsd covalent geometry : bond 0.00307 (15498) covalent geometry : angle 0.59577 (21000) hydrogen bonds : bond 0.03449 ( 468) hydrogen bonds : angle 6.44324 ( 1152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 189 time to evaluate : 0.402 Fit side-chains REVERT: A 107 GLN cc_start: 0.8527 (mm110) cc_final: 0.7832 (mt0) REVERT: A 144 HIS cc_start: 0.7502 (t70) cc_final: 0.6061 (m-70) REVERT: A 191 ASP cc_start: 0.8079 (t70) cc_final: 0.7693 (t0) REVERT: B 68 TYR cc_start: 0.7860 (t80) cc_final: 0.7307 (t80) REVERT: B 204 ASP cc_start: 0.7996 (p0) cc_final: 0.7617 (p0) REVERT: C 98 MET cc_start: 0.8153 (tpp) cc_final: 0.7673 (tpt) REVERT: C 105 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7427 (tm-30) REVERT: C 114 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8335 (mttm) REVERT: C 190 TYR cc_start: 0.8880 (t80) cc_final: 0.8602 (t80) REVERT: C 191 ASP cc_start: 0.7877 (t70) cc_final: 0.7640 (t0) REVERT: C 328 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7399 (t0) REVERT: D 142 GLN cc_start: 0.5168 (tt0) cc_final: 0.4954 (tt0) REVERT: D 144 HIS cc_start: 0.7524 (t70) cc_final: 0.6107 (m-70) REVERT: D 191 ASP cc_start: 0.8129 (t70) cc_final: 0.7715 (t0) REVERT: E 204 ASP cc_start: 0.7981 (p0) cc_final: 0.7597 (p0) REVERT: F 98 MET cc_start: 0.8145 (tpp) cc_final: 0.7629 (tpt) REVERT: F 105 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7400 (tm-30) REVERT: F 114 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8270 (mttm) REVERT: F 190 TYR cc_start: 0.8894 (t80) cc_final: 0.8591 (t80) REVERT: F 191 ASP cc_start: 0.7901 (t70) cc_final: 0.7688 (t0) REVERT: F 328 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7404 (t0) outliers start: 66 outliers final: 57 residues processed: 242 average time/residue: 0.1145 time to fit residues: 41.4686 Evaluate side-chains 240 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 367 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 84 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 142 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS D 338 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 HIS ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.141018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110197 restraints weight = 22815.823| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.64 r_work: 0.3150 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15498 Z= 0.181 Angle : 0.631 11.333 21000 Z= 0.318 Chirality : 0.047 0.177 2448 Planarity : 0.004 0.036 2736 Dihedral : 4.774 18.817 2136 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.86 % Allowed : 14.29 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.18), residues: 1998 helix: -1.12 (0.37), residues: 210 sheet: -0.26 (0.20), residues: 606 loop : -1.45 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 155 TYR 0.035 0.002 TYR C 68 PHE 0.015 0.002 PHE A 253 TRP 0.010 0.002 TRP D 109 HIS 0.003 0.001 HIS E 144 Details of bonding type rmsd covalent geometry : bond 0.00422 (15498) covalent geometry : angle 0.63129 (21000) hydrogen bonds : bond 0.03664 ( 468) hydrogen bonds : angle 6.56726 ( 1152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 197 time to evaluate : 0.571 Fit side-chains REVERT: A 54 MET cc_start: 0.6144 (mmt) cc_final: 0.5854 (mtt) REVERT: A 107 GLN cc_start: 0.8635 (mm110) cc_final: 0.7926 (mt0) REVERT: A 144 HIS cc_start: 0.7594 (t70) cc_final: 0.6650 (m-70) REVERT: A 191 ASP cc_start: 0.8367 (t70) cc_final: 0.7956 (t0) REVERT: B 68 TYR cc_start: 0.7849 (t80) cc_final: 0.7351 (t80) REVERT: B 153 LYS cc_start: 0.8008 (tptt) cc_final: 0.7793 (tptt) REVERT: B 204 ASP cc_start: 0.8249 (p0) cc_final: 0.7897 (p0) REVERT: C 105 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7476 (tm-30) REVERT: C 114 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8361 (mttm) REVERT: C 124 ASP cc_start: 0.8195 (t0) cc_final: 0.7980 (t70) REVERT: C 190 TYR cc_start: 0.9009 (t80) cc_final: 0.8704 (t80) REVERT: C 191 ASP cc_start: 0.8208 (t70) cc_final: 0.7991 (t0) REVERT: C 328 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7661 (t0) REVERT: D 54 MET cc_start: 0.6150 (mmt) cc_final: 0.5827 (mtt) REVERT: D 144 HIS cc_start: 0.7602 (t70) cc_final: 0.6300 (m90) REVERT: D 199 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8587 (mm110) REVERT: D 337 GLU cc_start: 0.7607 (tt0) cc_final: 0.7302 (tm-30) REVERT: E 144 HIS cc_start: 0.8048 (t-170) cc_final: 0.6742 (m-70) REVERT: E 153 LYS cc_start: 0.8100 (tptt) cc_final: 0.7872 (tptt) REVERT: E 204 ASP cc_start: 0.8245 (p0) cc_final: 0.7901 (p0) REVERT: F 105 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7539 (tm-30) REVERT: F 114 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8363 (mttm) REVERT: F 190 TYR cc_start: 0.9002 (t80) cc_final: 0.8707 (t80) REVERT: F 191 ASP cc_start: 0.8230 (t70) cc_final: 0.7989 (t0) REVERT: F 328 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7632 (t0) outliers start: 65 outliers final: 57 residues processed: 250 average time/residue: 0.1153 time to fit residues: 43.0783 Evaluate side-chains 251 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 192 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 367 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 138 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 115 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.142419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111530 restraints weight = 22871.576| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.68 r_work: 0.3169 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15498 Z= 0.146 Angle : 0.604 11.201 21000 Z= 0.304 Chirality : 0.046 0.187 2448 Planarity : 0.004 0.035 2736 Dihedral : 4.641 18.298 2136 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 3.68 % Allowed : 14.59 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.18), residues: 1998 helix: -1.08 (0.37), residues: 210 sheet: -0.24 (0.21), residues: 606 loop : -1.43 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 155 TYR 0.028 0.002 TYR C 68 PHE 0.014 0.001 PHE A 253 TRP 0.010 0.002 TRP D 109 HIS 0.002 0.000 HIS E 144 Details of bonding type rmsd covalent geometry : bond 0.00339 (15498) covalent geometry : angle 0.60450 (21000) hydrogen bonds : bond 0.03504 ( 468) hydrogen bonds : angle 6.45210 ( 1152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 191 time to evaluate : 0.589 Fit side-chains REVERT: A 54 MET cc_start: 0.5896 (mmt) cc_final: 0.5693 (mtt) REVERT: A 107 GLN cc_start: 0.8530 (mm110) cc_final: 0.7769 (mt0) REVERT: A 144 HIS cc_start: 0.7611 (t70) cc_final: 0.6674 (m-70) REVERT: A 191 ASP cc_start: 0.8050 (t70) cc_final: 0.7631 (t0) REVERT: B 68 TYR cc_start: 0.7662 (t80) cc_final: 0.7169 (t80) REVERT: B 153 LYS cc_start: 0.7920 (tptt) cc_final: 0.7715 (tptt) REVERT: B 204 ASP cc_start: 0.7993 (p0) cc_final: 0.7598 (p0) REVERT: C 105 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7260 (tm-30) REVERT: C 114 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8300 (mttm) REVERT: C 190 TYR cc_start: 0.8884 (t80) cc_final: 0.8525 (t80) REVERT: C 191 ASP cc_start: 0.7933 (t70) cc_final: 0.7705 (t0) REVERT: C 328 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7414 (t0) REVERT: D 54 MET cc_start: 0.5918 (mmt) cc_final: 0.5663 (mtt) REVERT: D 144 HIS cc_start: 0.7616 (t70) cc_final: 0.6300 (m-70) REVERT: D 337 GLU cc_start: 0.7361 (tt0) cc_final: 0.7093 (tm-30) REVERT: E 153 LYS cc_start: 0.7940 (tptt) cc_final: 0.7733 (tptt) REVERT: E 204 ASP cc_start: 0.7991 (p0) cc_final: 0.7605 (p0) REVERT: F 105 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7390 (tm-30) REVERT: F 114 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8215 (mttm) REVERT: F 190 TYR cc_start: 0.8924 (t80) cc_final: 0.8597 (t80) REVERT: F 191 ASP cc_start: 0.7891 (t70) cc_final: 0.7644 (t0) REVERT: F 328 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7389 (t0) outliers start: 62 outliers final: 57 residues processed: 241 average time/residue: 0.1161 time to fit residues: 42.0602 Evaluate side-chains 246 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 187 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 367 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 69 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 161 optimal weight: 0.0570 chunk 44 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS C 107 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 HIS ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.142891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112348 restraints weight = 22634.997| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.67 r_work: 0.3192 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15498 Z= 0.138 Angle : 0.598 11.142 21000 Z= 0.301 Chirality : 0.046 0.177 2448 Planarity : 0.004 0.037 2736 Dihedral : 4.561 17.205 2136 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.62 % Allowed : 14.71 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.18), residues: 1998 helix: -1.04 (0.37), residues: 210 sheet: -0.24 (0.21), residues: 606 loop : -1.40 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 155 TYR 0.028 0.002 TYR D 68 PHE 0.013 0.001 PHE A 253 TRP 0.009 0.002 TRP D 109 HIS 0.002 0.000 HIS E 144 Details of bonding type rmsd covalent geometry : bond 0.00320 (15498) covalent geometry : angle 0.59802 (21000) hydrogen bonds : bond 0.03430 ( 468) hydrogen bonds : angle 6.41180 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3710.20 seconds wall clock time: 64 minutes 7.94 seconds (3847.94 seconds total)