Starting phenix.real_space_refine on Sat Feb 7 21:31:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dn6_47031/02_2026/9dn6_47031_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dn6_47031/02_2026/9dn6_47031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dn6_47031/02_2026/9dn6_47031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dn6_47031/02_2026/9dn6_47031.map" model { file = "/net/cci-nas-00/data/ceres_data/9dn6_47031/02_2026/9dn6_47031_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dn6_47031/02_2026/9dn6_47031_neut.cif" } resolution = 4.0 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9494 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 92 5.16 5 C 9142 2.51 5 N 2436 2.21 5 O 2668 1.98 5 H 14193 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28531 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2190 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "B" Number of atoms: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2190 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "C" Number of atoms: 12076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 12076 Classifications: {'peptide': 753} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 711} Chain breaks: 7 Chain: "D" Number of atoms: 12075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 12075 Classifications: {'peptide': 753} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 711} Chain breaks: 7 Time building chain proxies: 5.74, per 1000 atoms: 0.20 Number of scatterers: 28531 At special positions: 0 Unit cell: (176.55, 93.09, 151.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 O 2668 8.00 N 2436 7.00 C 9142 6.00 H 14193 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 26 " distance=2.03 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS C 188 " distance=2.03 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 207 " distance=2.03 Simple disulfide: pdb=" SG CYS C 208 " - pdb=" SG CYS C 216 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 225 " - pdb=" SG CYS C 237 " distance=2.59 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 237 " distance=2.29 Simple disulfide: pdb=" SG CYS C 241 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 304 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 312 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 435 " - pdb=" SG CYS C 468 " distance=2.04 Simple disulfide: pdb=" SG CYS C 647 " - pdb=" SG CYS C 860 " distance=2.03 Simple disulfide: pdb=" SG CYS C 786 " - pdb=" SG CYS C 795 " distance=2.03 Simple disulfide: pdb=" SG CYS D 8 " - pdb=" SG CYS D 26 " distance=2.03 Simple disulfide: pdb=" SG CYS D 169 " - pdb=" SG CYS D 188 " distance=2.03 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 196 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS D 208 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS D 212 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 225 " - pdb=" SG CYS D 237 " distance=2.60 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 237 " distance=2.29 Simple disulfide: pdb=" SG CYS D 241 " - pdb=" SG CYS D 253 " distance=2.03 Simple disulfide: pdb=" SG CYS D 259 " - pdb=" SG CYS D 284 " distance=2.03 Simple disulfide: pdb=" SG CYS D 288 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 304 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 312 " - pdb=" SG CYS D 333 " distance=2.03 Simple disulfide: pdb=" SG CYS D 435 " - pdb=" SG CYS D 468 " distance=2.04 Simple disulfide: pdb=" SG CYS D 647 " - pdb=" SG CYS D 860 " distance=2.03 Simple disulfide: pdb=" SG CYS D 786 " - pdb=" SG CYS D 795 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 845.9 milliseconds 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 28 sheets defined 25.8% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 Processing helix chain 'A' and resid 17 through 32 removed outlier: 3.739A pdb=" N LYS A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 52 removed outlier: 3.526A pdb=" N GLU A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 87 removed outlier: 4.303A pdb=" N TYR A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TRP A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 75 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 Processing helix chain 'A' and resid 111 through 130 removed outlier: 3.670A pdb=" N GLU A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.768A pdb=" N LYS B 21 " --> pdb=" O ASP B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 52 removed outlier: 3.539A pdb=" N GLU B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 87 removed outlier: 4.307A pdb=" N TYR B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TRP B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 75 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 110 Processing helix chain 'B' and resid 111 through 130 removed outlier: 3.665A pdb=" N GLU B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 24 removed outlier: 3.500A pdb=" N GLU C 24 " --> pdb=" O HIS C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 removed outlier: 3.926A pdb=" N PHE C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 221 through 225 removed outlier: 4.255A pdb=" N CYS C 225 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.718A pdb=" N CYS C 259 " --> pdb=" O ASN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 323 through 330 removed outlier: 3.579A pdb=" N ALA C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 358 Processing helix chain 'C' and resid 435 through 447 removed outlier: 3.798A pdb=" N ILE C 439 " --> pdb=" O CYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 452 removed outlier: 4.069A pdb=" N GLN C 452 " --> pdb=" O LYS C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 638 through 642 Processing helix chain 'C' and resid 863 through 870 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 42 through 47 removed outlier: 3.924A pdb=" N PHE D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 75 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'D' and resid 221 through 225 removed outlier: 4.263A pdb=" N CYS D 225 " --> pdb=" O PRO D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.729A pdb=" N CYS D 259 " --> pdb=" O ASN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 318 Processing helix chain 'D' and resid 323 through 330 removed outlier: 3.551A pdb=" N ALA D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 358 Processing helix chain 'D' and resid 435 through 447 removed outlier: 3.776A pdb=" N ILE D 439 " --> pdb=" O CYS D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 452 removed outlier: 4.064A pdb=" N GLN D 452 " --> pdb=" O LYS D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'D' and resid 496 through 498 No H-bonds generated for 'chain 'D' and resid 496 through 498' Processing helix chain 'D' and resid 638 through 642 Processing helix chain 'D' and resid 863 through 870 Processing sheet with id=AA1, first strand: chain 'C' and resid 7 through 9 removed outlier: 7.127A pdb=" N CYS C 8 " --> pdb=" O GLU C 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.652A pdb=" N ILE C 13 " --> pdb=" O LEU C 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 119 through 122 removed outlier: 7.098A pdb=" N GLU C 120 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU C 147 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 231 through 233 Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 312 Processing sheet with id=AA6, first strand: chain 'C' and resid 320 through 321 removed outlier: 9.528A pdb=" N LEU C 403 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE C 370 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 363 through 366 removed outlier: 10.099A pdb=" N GLU C 363 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N GLU C 391 " --> pdb=" O GLU C 363 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N SER C 365 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 475 through 477 removed outlier: 6.537A pdb=" N ARG C 488 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 485 " --> pdb=" O MET C 553 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 532 through 533 removed outlier: 4.066A pdb=" N GLY C 502 " --> pdb=" O LEU C 569 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 599 through 602 removed outlier: 6.511A pdb=" N LYS C 614 " --> pdb=" O PRO C 601 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 759 through 762 removed outlier: 3.665A pdb=" N HIS C 627 " --> pdb=" O CYS C 786 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS C 786 " --> pdb=" O HIS C 627 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 783 " --> pdb=" O ALA C 799 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 799 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 819 through 823 removed outlier: 3.823A pdb=" N VAL C 827 " --> pdb=" O PHE C 823 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 860 through 862 removed outlier: 4.043A pdb=" N VAL C 861 " --> pdb=" O TYR C 845 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR C 845 " --> pdb=" O VAL C 861 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU C 844 " --> pdb=" O THR C 889 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE C 886 " --> pdb=" O TRP C 897 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TRP C 897 " --> pdb=" O ILE C 886 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA C 888 " --> pdb=" O GLY C 895 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 860 through 862 removed outlier: 4.043A pdb=" N VAL C 861 " --> pdb=" O TYR C 845 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR C 845 " --> pdb=" O VAL C 861 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU C 844 " --> pdb=" O THR C 889 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 7 through 9 removed outlier: 7.125A pdb=" N CYS D 8 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 13 through 14 removed outlier: 6.656A pdb=" N ILE D 13 " --> pdb=" O LEU D 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 119 through 122 removed outlier: 7.095A pdb=" N GLU D 120 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU D 147 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 231 through 233 Processing sheet with id=AC1, first strand: chain 'D' and resid 311 through 312 Processing sheet with id=AC2, first strand: chain 'D' and resid 320 through 321 removed outlier: 9.525A pdb=" N LEU D 403 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE D 370 " --> pdb=" O LEU D 403 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 363 through 366 removed outlier: 10.086A pdb=" N GLU D 363 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N GLU D 391 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N SER D 365 " --> pdb=" O GLU D 391 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 475 through 477 removed outlier: 6.542A pdb=" N ARG D 488 " --> pdb=" O SER D 476 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 485 " --> pdb=" O MET D 553 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 532 through 533 removed outlier: 4.063A pdb=" N GLY D 502 " --> pdb=" O LEU D 569 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 599 through 602 removed outlier: 6.508A pdb=" N LYS D 614 " --> pdb=" O PRO D 601 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 759 through 762 removed outlier: 3.656A pdb=" N HIS D 627 " --> pdb=" O CYS D 786 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS D 786 " --> pdb=" O HIS D 627 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 783 " --> pdb=" O ALA D 799 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 799 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 819 through 823 removed outlier: 3.821A pdb=" N VAL D 827 " --> pdb=" O PHE D 823 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 860 through 862 removed outlier: 4.044A pdb=" N VAL D 861 " --> pdb=" O TYR D 845 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR D 845 " --> pdb=" O VAL D 861 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D 844 " --> pdb=" O THR D 889 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE D 886 " --> pdb=" O TRP D 897 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP D 897 " --> pdb=" O ILE D 886 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA D 888 " --> pdb=" O GLY D 895 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 860 through 862 removed outlier: 4.044A pdb=" N VAL D 861 " --> pdb=" O TYR D 845 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR D 845 " --> pdb=" O VAL D 861 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D 844 " --> pdb=" O THR D 889 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1095 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: 7.34 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 14127 1.04 - 1.24: 1911 1.24 - 1.44: 4419 1.44 - 1.64: 8286 1.64 - 1.84: 118 Bond restraints: 28861 Sorted by residual: bond pdb=" N VAL D 238 " pdb=" CA VAL D 238 " ideal model delta sigma weight residual 1.456 1.523 -0.067 1.23e-02 6.61e+03 2.97e+01 bond pdb=" N VAL C 238 " pdb=" CA VAL C 238 " ideal model delta sigma weight residual 1.456 1.516 -0.060 1.23e-02 6.61e+03 2.37e+01 bond pdb=" CA CYS D 237 " pdb=" C CYS D 237 " ideal model delta sigma weight residual 1.525 1.567 -0.042 1.25e-02 6.40e+03 1.13e+01 bond pdb=" N ARG D 236 " pdb=" CA ARG D 236 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.21e-02 6.83e+03 9.18e+00 bond pdb=" C CYS D 237 " pdb=" N VAL D 238 " ideal model delta sigma weight residual 1.333 1.370 -0.038 1.27e-02 6.20e+03 8.75e+00 ... (remaining 28856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.87: 52151 9.87 - 19.74: 9 19.74 - 29.60: 13 29.60 - 39.47: 19 39.47 - 49.34: 4 Bond angle restraints: 52196 Sorted by residual: angle pdb=" C ASN C 514 " pdb=" N VAL C 515 " pdb=" H VAL C 515 " ideal model delta sigma weight residual 124.17 74.82 49.34 3.00e+00 1.11e-01 2.71e+02 angle pdb=" C ASN D 514 " pdb=" N VAL D 515 " pdb=" H VAL D 515 " ideal model delta sigma weight residual 124.17 74.83 49.33 3.00e+00 1.11e-01 2.70e+02 angle pdb=" CA VAL C 515 " pdb=" N VAL C 515 " pdb=" H VAL C 515 " ideal model delta sigma weight residual 113.87 65.10 48.77 3.00e+00 1.11e-01 2.64e+02 angle pdb=" CA VAL D 515 " pdb=" N VAL D 515 " pdb=" H VAL D 515 " ideal model delta sigma weight residual 113.87 65.10 48.77 3.00e+00 1.11e-01 2.64e+02 angle pdb=" C PRO A 56 " pdb=" CA PRO A 56 " pdb=" HA PRO A 56 " ideal model delta sigma weight residual 109.00 70.24 38.76 3.00e+00 1.11e-01 1.67e+02 ... (remaining 52191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 11930 18.08 - 36.17: 1263 36.17 - 54.25: 390 54.25 - 72.34: 64 72.34 - 90.42: 26 Dihedral angle restraints: 13673 sinusoidal: 7504 harmonic: 6169 Sorted by residual: dihedral pdb=" CA ASP D 542 " pdb=" C ASP D 542 " pdb=" N PRO D 543 " pdb=" CA PRO D 543 " ideal model delta harmonic sigma weight residual -180.00 -127.53 -52.47 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CB CYS D 225 " pdb=" SG CYS D 225 " pdb=" SG CYS D 237 " pdb=" CB CYS D 237 " ideal model delta sinusoidal sigma weight residual -86.00 -176.42 90.42 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS C 225 " pdb=" SG CYS C 225 " pdb=" SG CYS C 237 " pdb=" CB CYS C 237 " ideal model delta sinusoidal sigma weight residual 93.00 -176.91 -90.09 1 1.00e+01 1.00e-02 9.61e+01 ... (remaining 13670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2022 0.091 - 0.182: 134 0.182 - 0.273: 3 0.273 - 0.364: 5 0.364 - 0.455: 2 Chirality restraints: 2166 Sorted by residual: chirality pdb=" CA PRO B 56 " pdb=" N PRO B 56 " pdb=" C PRO B 56 " pdb=" CB PRO B 56 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA PRO A 56 " pdb=" N PRO A 56 " pdb=" C PRO A 56 " pdb=" CB PRO A 56 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA LYS C 310 " pdb=" N LYS C 310 " pdb=" C LYS C 310 " pdb=" CB LYS C 310 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 2163 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 236 " -0.852 9.50e-02 1.11e+02 5.16e-01 4.25e+03 pdb=" NE ARG D 236 " -0.387 2.00e-02 2.50e+03 pdb=" CZ ARG D 236 " -0.100 2.00e-02 2.50e+03 pdb=" NH1 ARG D 236 " 0.065 2.00e-02 2.50e+03 pdb=" NH2 ARG D 236 " 0.036 2.00e-02 2.50e+03 pdb="HH11 ARG D 236 " 0.797 2.00e-02 2.50e+03 pdb="HH12 ARG D 236 " -0.550 2.00e-02 2.50e+03 pdb="HH21 ARG D 236 " 0.612 2.00e-02 2.50e+03 pdb="HH22 ARG D 236 " -0.436 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 236 " 1.044 9.50e-02 1.11e+02 5.02e-01 3.06e+03 pdb=" NE ARG C 236 " 0.341 2.00e-02 2.50e+03 pdb=" CZ ARG C 236 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG C 236 " -0.053 2.00e-02 2.50e+03 pdb=" NH2 ARG C 236 " -0.040 2.00e-02 2.50e+03 pdb="HH11 ARG C 236 " -0.732 2.00e-02 2.50e+03 pdb="HH12 ARG C 236 " 0.526 2.00e-02 2.50e+03 pdb="HH21 ARG C 236 " -0.420 2.00e-02 2.50e+03 pdb="HH22 ARG C 236 " 0.246 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 542 " 0.138 5.00e-02 4.00e+02 1.99e-01 6.35e+01 pdb=" N PRO C 543 " -0.344 5.00e-02 4.00e+02 pdb=" CA PRO C 543 " 0.118 5.00e-02 4.00e+02 pdb=" CD PRO C 543 " 0.087 5.00e-02 4.00e+02 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 1062 2.12 - 2.74: 53189 2.74 - 3.36: 84628 3.36 - 3.98: 105112 3.98 - 4.60: 161622 Nonbonded interactions: 405613 Sorted by model distance: nonbonded pdb=" OE1 GLN D 406 " pdb=" H LYS D 433 " model vdw 1.505 2.450 nonbonded pdb=" OE1 GLN D 513 " pdb="HE22 GLN D 561 " model vdw 1.507 2.450 nonbonded pdb=" OE1 GLN C 513 " pdb="HE22 GLN C 561 " model vdw 1.508 2.450 nonbonded pdb=" OE1 GLU D 517 " pdb=" H GLU D 517 " model vdw 1.532 2.450 nonbonded pdb=" OE1 GLU C 517 " pdb=" H GLU C 517 " model vdw 1.533 2.450 ... (remaining 405608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 5 through 828 or (resid 829 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 830 through 905)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.190 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 28.910 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 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 0.567 14700 Z= 0.409 Angle : 0.877 47.900 19908 Z= 0.453 Chirality : 0.047 0.455 2166 Planarity : 0.009 0.224 2544 Dihedral : 16.434 89.700 5524 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.46 % Allowed : 12.02 % Favored : 87.51 % Rotamer: Outliers : 0.44 % Allowed : 20.52 % Favored : 79.04 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -2.09 (0.21), residues: 1730 helix: 0.67 (0.27), residues: 356 sheet: -1.80 (0.29), residues: 306 loop : -2.08 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 236 TYR 0.010 0.001 TYR C 374 PHE 0.009 0.001 PHE D 51 TRP 0.022 0.002 TRP D 632 HIS 0.003 0.001 HIS D 263 Details of bonding type rmsd covalent geometry : bond 0.00390 (14668) covalent geometry : angle 0.71189 (19844) SS BOND : bond 0.15540 ( 32) SS BOND : angle 9.07316 ( 64) hydrogen bonds : bond 0.23823 ( 404) hydrogen bonds : angle 9.13533 ( 1095) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.756 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 100 average time/residue: 0.2484 time to fit residues: 38.9134 Evaluate side-chains 97 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 882 TYR Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 882 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 513 GLN C 561 GLN D 513 GLN D 561 GLN D 829 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.117015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.084120 restraints weight = 107617.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.086825 restraints weight = 64474.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.087886 restraints weight = 46934.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.088598 restraints weight = 41923.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.088838 restraints weight = 36332.333| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14700 Z= 0.173 Angle : 0.668 17.769 19908 Z= 0.350 Chirality : 0.047 0.438 2166 Planarity : 0.006 0.147 2544 Dihedral : 5.674 51.635 1932 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.97 % Favored : 87.57 % Rotamer: Outliers : 1.31 % Allowed : 20.09 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -2.40 (0.20), residues: 1730 helix: 0.38 (0.26), residues: 362 sheet: -2.25 (0.26), residues: 320 loop : -2.19 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 236 TYR 0.014 0.001 TYR D 882 PHE 0.011 0.001 PHE D 903 TRP 0.013 0.001 TRP D 414 HIS 0.004 0.001 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00386 (14668) covalent geometry : angle 0.66152 (19844) SS BOND : bond 0.00766 ( 32) SS BOND : angle 1.75286 ( 64) hydrogen bonds : bond 0.05673 ( 404) hydrogen bonds : angle 7.45161 ( 1095) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.764 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7407 (tpp) cc_final: 0.7126 (tpp) REVERT: B 78 MET cc_start: 0.7427 (tpp) cc_final: 0.7141 (tpp) REVERT: C 132 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.7046 (m-30) REVERT: D 132 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.7061 (m-30) outliers start: 21 outliers final: 17 residues processed: 110 average time/residue: 0.2359 time to fit residues: 40.9744 Evaluate side-chains 109 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 786 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 401 TYR Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 786 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 71 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.116226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.084293 restraints weight = 107875.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.085020 restraints weight = 67707.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.086689 restraints weight = 53148.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.087937 restraints weight = 43337.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.088006 restraints weight = 37401.640| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14700 Z= 0.196 Angle : 0.654 18.075 19908 Z= 0.344 Chirality : 0.047 0.447 2166 Planarity : 0.006 0.127 2544 Dihedral : 5.418 52.662 1922 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.46 % Allowed : 13.24 % Favored : 86.30 % Rotamer: Outliers : 2.30 % Allowed : 19.84 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -2.54 (0.20), residues: 1730 helix: 0.33 (0.27), residues: 362 sheet: -2.37 (0.26), residues: 320 loop : -2.30 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 236 TYR 0.011 0.001 TYR C 60 PHE 0.014 0.001 PHE C 51 TRP 0.014 0.002 TRP B 25 HIS 0.003 0.001 HIS D 263 Details of bonding type rmsd covalent geometry : bond 0.00437 (14668) covalent geometry : angle 0.64572 (19844) SS BOND : bond 0.00704 ( 32) SS BOND : angle 1.92000 ( 64) hydrogen bonds : bond 0.04733 ( 404) hydrogen bonds : angle 6.87547 ( 1095) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.741 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7400 (tpp) cc_final: 0.7188 (tpp) REVERT: B 78 MET cc_start: 0.7410 (tpp) cc_final: 0.7180 (tpp) REVERT: C 11 MET cc_start: 0.8916 (pmm) cc_final: 0.8444 (pmm) REVERT: D 12 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.7925 (p0) outliers start: 37 outliers final: 29 residues processed: 118 average time/residue: 0.2351 time to fit residues: 44.3839 Evaluate side-chains 116 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 786 CYS Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 401 TYR Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 806 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 100 optimal weight: 50.0000 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.0000 chunk 160 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.117588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.086813 restraints weight = 107243.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.086265 restraints weight = 67056.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.088039 restraints weight = 51694.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.091347 restraints weight = 42155.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.091143 restraints weight = 34298.600| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14700 Z= 0.124 Angle : 0.604 17.886 19908 Z= 0.316 Chirality : 0.046 0.438 2166 Planarity : 0.005 0.118 2544 Dihedral : 5.272 53.019 1922 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.29 % Favored : 89.36 % Rotamer: Outliers : 1.74 % Allowed : 20.90 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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 (0.20), residues: 1730 helix: 0.59 (0.27), residues: 362 sheet: -2.30 (0.26), residues: 320 loop : -2.22 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 181 TYR 0.008 0.001 TYR C 374 PHE 0.010 0.001 PHE D 51 TRP 0.013 0.001 TRP C 414 HIS 0.003 0.001 HIS D 820 Details of bonding type rmsd covalent geometry : bond 0.00279 (14668) covalent geometry : angle 0.60126 (19844) SS BOND : bond 0.00651 ( 32) SS BOND : angle 1.21188 ( 64) hydrogen bonds : bond 0.04024 ( 404) hydrogen bonds : angle 6.54593 ( 1095) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.801 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7371 (tpp) cc_final: 0.7098 (tpp) REVERT: B 78 MET cc_start: 0.7388 (tpp) cc_final: 0.7118 (tpp) REVERT: C 11 MET cc_start: 0.8849 (pmm) cc_final: 0.8361 (pmm) REVERT: D 11 MET cc_start: 0.8831 (pmm) cc_final: 0.8375 (pmm) REVERT: D 12 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.7977 (p0) REVERT: D 132 ASP cc_start: 0.7325 (m-30) cc_final: 0.7057 (m-30) REVERT: D 477 TYR cc_start: 0.8800 (t80) cc_final: 0.8406 (t80) outliers start: 28 outliers final: 23 residues processed: 117 average time/residue: 0.2269 time to fit residues: 42.4307 Evaluate side-chains 118 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 786 CYS Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 401 TYR Chi-restraints excluded: chain D residue 429 HIS Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 786 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 106 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 145 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.117505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.087344 restraints weight = 107534.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.088429 restraints weight = 59844.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.089739 restraints weight = 47218.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.090594 restraints weight = 38416.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.090780 restraints weight = 34469.054| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14700 Z= 0.129 Angle : 0.598 17.932 19908 Z= 0.313 Chirality : 0.046 0.437 2166 Planarity : 0.005 0.114 2544 Dihedral : 5.180 53.285 1922 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.16 % Favored : 88.50 % Rotamer: Outliers : 2.05 % Allowed : 20.77 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -2.33 (0.20), residues: 1730 helix: 0.69 (0.27), residues: 362 sheet: -2.26 (0.26), residues: 320 loop : -2.23 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 181 TYR 0.018 0.001 TYR C 492 PHE 0.010 0.001 PHE C 51 TRP 0.020 0.001 TRP D 414 HIS 0.003 0.001 HIS D 820 Details of bonding type rmsd covalent geometry : bond 0.00291 (14668) covalent geometry : angle 0.59483 (19844) SS BOND : bond 0.00486 ( 32) SS BOND : angle 1.18773 ( 64) hydrogen bonds : bond 0.03880 ( 404) hydrogen bonds : angle 6.34927 ( 1095) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.710 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7329 (tpp) cc_final: 0.7036 (tpp) REVERT: B 78 MET cc_start: 0.7396 (tpp) cc_final: 0.7108 (tpp) REVERT: C 11 MET cc_start: 0.8896 (pmm) cc_final: 0.8585 (pmm) REVERT: C 132 ASP cc_start: 0.7271 (m-30) cc_final: 0.7060 (m-30) REVERT: C 315 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6818 (pp) REVERT: D 11 MET cc_start: 0.8857 (pmm) cc_final: 0.8413 (pmm) REVERT: D 12 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7935 (p0) REVERT: D 132 ASP cc_start: 0.7387 (m-30) cc_final: 0.7086 (m-30) REVERT: D 315 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6837 (pp) REVERT: D 477 TYR cc_start: 0.8795 (t80) cc_final: 0.8425 (t80) outliers start: 33 outliers final: 26 residues processed: 125 average time/residue: 0.2195 time to fit residues: 44.4443 Evaluate side-chains 128 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 429 HIS Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 786 CYS Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 401 TYR Chi-restraints excluded: chain D residue 429 HIS Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 786 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 131 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.114399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.083597 restraints weight = 108446.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.083133 restraints weight = 67910.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.084791 restraints weight = 53355.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.085556 restraints weight = 44104.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.085771 restraints weight = 39954.346| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 14700 Z= 0.292 Angle : 0.693 18.164 19908 Z= 0.369 Chirality : 0.048 0.452 2166 Planarity : 0.006 0.112 2544 Dihedral : 5.423 52.757 1922 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.46 % Allowed : 14.62 % Favored : 84.91 % Rotamer: Outliers : 2.99 % Allowed : 20.96 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -2.63 (0.20), residues: 1730 helix: 0.41 (0.27), residues: 362 sheet: -2.35 (0.26), residues: 318 loop : -2.45 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 181 TYR 0.015 0.002 TYR D 60 PHE 0.015 0.002 PHE A 74 TRP 0.017 0.002 TRP D 414 HIS 0.004 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00654 (14668) covalent geometry : angle 0.68937 (19844) SS BOND : bond 0.00716 ( 32) SS BOND : angle 1.44655 ( 64) hydrogen bonds : bond 0.04282 ( 404) hydrogen bonds : angle 6.58773 ( 1095) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 94 time to evaluate : 0.797 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 MET cc_start: 0.7514 (tpp) cc_final: 0.7246 (tpp) REVERT: C 11 MET cc_start: 0.8914 (pmm) cc_final: 0.8541 (pmm) REVERT: D 11 MET cc_start: 0.9005 (pmm) cc_final: 0.8536 (pmm) REVERT: D 12 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.7753 (p0) REVERT: D 132 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7169 (m-30) outliers start: 48 outliers final: 39 residues processed: 128 average time/residue: 0.2214 time to fit residues: 45.0207 Evaluate side-chains 132 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 91 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 429 HIS Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 786 CYS Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 401 TYR Chi-restraints excluded: chain D residue 429 HIS Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 806 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 97 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.115496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.082663 restraints weight = 109114.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.084513 restraints weight = 63418.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.085583 restraints weight = 47531.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.086575 restraints weight = 43210.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.086707 restraints weight = 36743.419| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14700 Z= 0.199 Angle : 0.642 18.110 19908 Z= 0.340 Chirality : 0.047 0.445 2166 Planarity : 0.005 0.108 2544 Dihedral : 5.403 53.248 1922 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.46 % Allowed : 12.43 % Favored : 87.11 % Rotamer: Outliers : 2.61 % Allowed : 21.39 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -2.54 (0.20), residues: 1730 helix: 0.56 (0.27), residues: 362 sheet: -2.31 (0.26), residues: 328 loop : -2.41 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 389 TYR 0.010 0.001 TYR C 492 PHE 0.013 0.001 PHE D 51 TRP 0.018 0.002 TRP D 414 HIS 0.007 0.001 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00443 (14668) covalent geometry : angle 0.63879 (19844) SS BOND : bond 0.00540 ( 32) SS BOND : angle 1.25809 ( 64) hydrogen bonds : bond 0.04022 ( 404) hydrogen bonds : angle 6.35033 ( 1095) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 0.776 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 11 MET cc_start: 0.8930 (pmm) cc_final: 0.8595 (pmm) REVERT: C 132 ASP cc_start: 0.7425 (m-30) cc_final: 0.7215 (m-30) REVERT: C 251 TRP cc_start: 0.8336 (OUTLIER) cc_final: 0.6727 (t-100) REVERT: D 11 MET cc_start: 0.9011 (pmm) cc_final: 0.8596 (pmm) REVERT: D 12 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.7684 (p0) REVERT: D 132 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7073 (m-30) REVERT: D 251 TRP cc_start: 0.8420 (OUTLIER) cc_final: 0.6809 (t-100) outliers start: 42 outliers final: 36 residues processed: 131 average time/residue: 0.2184 time to fit residues: 45.9018 Evaluate side-chains 137 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 251 TRP Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 429 HIS Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 21 HIS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 401 TYR Chi-restraints excluded: chain D residue 429 HIS Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 806 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 171 optimal weight: 50.0000 chunk 172 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.115563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.082869 restraints weight = 109653.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.084183 restraints weight = 66304.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.085703 restraints weight = 50129.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.086448 restraints weight = 43568.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.086550 restraints weight = 38777.065| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14700 Z= 0.192 Angle : 0.636 18.000 19908 Z= 0.336 Chirality : 0.046 0.445 2166 Planarity : 0.005 0.105 2544 Dihedral : 5.366 53.508 1922 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.46 % Allowed : 13.64 % Favored : 85.90 % Rotamer: Outliers : 2.92 % Allowed : 21.64 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -2.48 (0.20), residues: 1730 helix: 0.65 (0.28), residues: 362 sheet: -2.35 (0.27), residues: 322 loop : -2.36 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 181 TYR 0.010 0.001 TYR C 232 PHE 0.014 0.001 PHE C 51 TRP 0.015 0.002 TRP C 414 HIS 0.014 0.001 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00432 (14668) covalent geometry : angle 0.63331 (19844) SS BOND : bond 0.00519 ( 32) SS BOND : angle 1.22569 ( 64) hydrogen bonds : bond 0.03942 ( 404) hydrogen bonds : angle 6.23123 ( 1095) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 97 time to evaluate : 0.785 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7480 (tpp) cc_final: 0.7116 (tpp) REVERT: C 11 MET cc_start: 0.8914 (pmm) cc_final: 0.8584 (pmm) REVERT: C 251 TRP cc_start: 0.8425 (OUTLIER) cc_final: 0.6830 (t-100) REVERT: D 11 MET cc_start: 0.8960 (pmm) cc_final: 0.8504 (pmm) REVERT: D 12 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7667 (p0) REVERT: D 132 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7047 (m-30) REVERT: D 251 TRP cc_start: 0.8424 (OUTLIER) cc_final: 0.6772 (t-100) outliers start: 47 outliers final: 43 residues processed: 129 average time/residue: 0.2282 time to fit residues: 47.5496 Evaluate side-chains 142 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 95 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 251 TRP Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 429 HIS Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 786 CYS Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 21 HIS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 232 TYR Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 401 TYR Chi-restraints excluded: chain D residue 429 HIS Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 806 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 25 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 122 optimal weight: 0.1980 chunk 69 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.117453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.085083 restraints weight = 109393.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.087061 restraints weight = 66840.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.088051 restraints weight = 47087.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.088750 restraints weight = 42582.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.088954 restraints weight = 38472.932| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14700 Z= 0.110 Angle : 0.594 17.858 19908 Z= 0.311 Chirality : 0.046 0.438 2166 Planarity : 0.005 0.101 2544 Dihedral : 5.211 54.054 1922 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.54 % Favored : 90.12 % Rotamer: Outliers : 2.18 % Allowed : 22.57 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -2.25 (0.20), residues: 1730 helix: 0.88 (0.28), residues: 362 sheet: -2.24 (0.27), residues: 322 loop : -2.21 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 58 TYR 0.011 0.001 TYR D 492 PHE 0.011 0.001 PHE C 51 TRP 0.017 0.001 TRP C 414 HIS 0.005 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00255 (14668) covalent geometry : angle 0.59226 (19844) SS BOND : bond 0.00378 ( 32) SS BOND : angle 1.04312 ( 64) hydrogen bonds : bond 0.03661 ( 404) hydrogen bonds : angle 5.92341 ( 1095) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.792 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 11 MET cc_start: 0.8917 (pmm) cc_final: 0.8589 (pmm) REVERT: C 251 TRP cc_start: 0.8368 (OUTLIER) cc_final: 0.6737 (t-100) REVERT: D 11 MET cc_start: 0.8929 (pmm) cc_final: 0.8517 (pmm) REVERT: D 12 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7752 (p0) REVERT: D 132 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6944 (m-30) REVERT: D 251 TRP cc_start: 0.8403 (OUTLIER) cc_final: 0.6813 (t-100) REVERT: D 477 TYR cc_start: 0.8800 (t80) cc_final: 0.8529 (t80) outliers start: 35 outliers final: 30 residues processed: 131 average time/residue: 0.2315 time to fit residues: 48.4426 Evaluate side-chains 135 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 251 TRP Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 429 HIS Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 21 HIS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 232 TYR Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 401 TYR Chi-restraints excluded: chain D residue 429 HIS Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 786 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 116 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 167 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.117146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.084304 restraints weight = 108585.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.086786 restraints weight = 64278.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.087403 restraints weight = 44739.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.088476 restraints weight = 43406.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.088593 restraints weight = 36947.122| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14700 Z= 0.120 Angle : 0.603 17.892 19908 Z= 0.313 Chirality : 0.046 0.438 2166 Planarity : 0.005 0.098 2544 Dihedral : 5.149 54.098 1922 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.10 % Favored : 88.55 % Rotamer: Outliers : 2.11 % Allowed : 22.95 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -2.21 (0.20), residues: 1730 helix: 0.87 (0.28), residues: 362 sheet: -2.20 (0.27), residues: 322 loop : -2.17 (0.20), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 118 TYR 0.010 0.001 TYR C 562 PHE 0.011 0.001 PHE A 43 TRP 0.015 0.001 TRP C 414 HIS 0.005 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00275 (14668) covalent geometry : angle 0.60074 (19844) SS BOND : bond 0.00470 ( 32) SS BOND : angle 1.14589 ( 64) hydrogen bonds : bond 0.03633 ( 404) hydrogen bonds : angle 5.87765 ( 1095) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.815 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 11 MET cc_start: 0.8927 (pmm) cc_final: 0.8622 (pmm) REVERT: C 251 TRP cc_start: 0.8408 (OUTLIER) cc_final: 0.6775 (t-100) REVERT: D 11 MET cc_start: 0.8935 (pmm) cc_final: 0.8517 (pmm) REVERT: D 12 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7731 (p0) REVERT: D 132 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6945 (m-30) REVERT: D 251 TRP cc_start: 0.8405 (OUTLIER) cc_final: 0.6837 (t-100) REVERT: D 477 TYR cc_start: 0.8831 (t80) cc_final: 0.8566 (t80) outliers start: 34 outliers final: 30 residues processed: 127 average time/residue: 0.2266 time to fit residues: 45.8647 Evaluate side-chains 133 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 251 TRP Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 429 HIS Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 21 HIS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 232 TYR Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 401 TYR Chi-restraints excluded: chain D residue 429 HIS Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 786 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 172 optimal weight: 20.0000 chunk 73 optimal weight: 0.0370 chunk 90 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.116867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.084293 restraints weight = 110173.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.087335 restraints weight = 62928.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.087590 restraints weight = 45678.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.088203 restraints weight = 42256.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.088393 restraints weight = 39491.898| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14700 Z= 0.134 Angle : 0.595 18.003 19908 Z= 0.312 Chirality : 0.046 0.440 2166 Planarity : 0.005 0.095 2544 Dihedral : 5.105 54.128 1922 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.50 % Favored : 88.15 % Rotamer: Outliers : 2.24 % Allowed : 22.76 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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: -2.19 (0.20), residues: 1730 helix: 0.90 (0.28), residues: 362 sheet: -2.20 (0.27), residues: 322 loop : -2.16 (0.20), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 118 TYR 0.015 0.001 TYR C 562 PHE 0.010 0.001 PHE C 51 TRP 0.013 0.001 TRP B 25 HIS 0.004 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00309 (14668) covalent geometry : angle 0.59192 (19844) SS BOND : bond 0.00514 ( 32) SS BOND : angle 1.16236 ( 64) hydrogen bonds : bond 0.03598 ( 404) hydrogen bonds : angle 5.82441 ( 1095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3988.97 seconds wall clock time: 69 minutes 7.56 seconds (4147.56 seconds total)