Starting phenix.real_space_refine on Wed Mar 4 10:54:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwf_26831/03_2026/7uwf_26831.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwf_26831/03_2026/7uwf_26831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uwf_26831/03_2026/7uwf_26831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwf_26831/03_2026/7uwf_26831.map" model { file = "/net/cci-nas-00/data/ceres_data/7uwf_26831/03_2026/7uwf_26831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwf_26831/03_2026/7uwf_26831.cif" } resolution = 2.7 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= 0.011 sd= 0.274 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 94 5.16 5 C 8394 2.51 5 N 2306 2.21 5 O 2380 1.98 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13174 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2725 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 343} Unresolved chain links: 3 Chain breaks: 1 Unresolved chain link angles: 9 Unresolved chain link dihedrals: 12 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 5, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3862 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 32, 'TRANS': 486} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2725 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 343} Unresolved chain links: 3 Chain breaks: 1 Unresolved chain link angles: 9 Unresolved chain link dihedrals: 12 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 5, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3862 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 32, 'TRANS': 486} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 2.71, per 1000 atoms: 0.21 Number of scatterers: 13174 At special positions: 0 Unit cell: (93.984, 108.768, 107.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 94 16.00 O 2380 8.00 N 2306 7.00 C 8394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 556.0 milliseconds 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 16 sheets defined 52.4% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 322 through 327 removed outlier: 3.521A pdb=" N LEU A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'C' and resid 31 through 42 Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 86 through 101 removed outlier: 3.605A pdb=" N SER C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 119 Processing helix chain 'C' and resid 120 through 140 removed outlier: 3.506A pdb=" N GLN C 125 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL C 129 " --> pdb=" O GLN C 125 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 140 " --> pdb=" O GLN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 163 Processing helix chain 'C' and resid 165 through 186 removed outlier: 3.606A pdb=" N ARG C 170 " --> pdb=" O PRO C 166 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 191 through 206 Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.268A pdb=" N SER C 212 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 226 removed outlier: 3.930A pdb=" N SER C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG C 224 " --> pdb=" O PHE C 220 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 241 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 249 through 279 removed outlier: 5.338A pdb=" N LYS C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N HIS C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 327 Processing helix chain 'C' and resid 337 through 350 removed outlier: 3.579A pdb=" N ILE C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 388 Proline residue: C 370 - end of helix Processing helix chain 'C' and resid 389 through 393 removed outlier: 4.335A pdb=" N ARG C 393 " --> pdb=" O ARG C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 409 Proline residue: C 403 - end of helix Processing helix chain 'C' and resid 424 through 443 Processing helix chain 'C' and resid 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 451 through 467 removed outlier: 4.229A pdb=" N GLY C 455 " --> pdb=" O GLY C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 537 Processing helix chain 'C' and resid 541 through 561 Proline residue: C 554 - end of helix removed outlier: 4.065A pdb=" N GLN C 560 " --> pdb=" O VAL C 556 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN C 561 " --> pdb=" O MET C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 571 Processing helix chain 'C' and resid 572 through 589 Processing helix chain 'C' and resid 597 through 609 Processing helix chain 'C' and resid 613 through 632 Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 322 through 327 removed outlier: 3.522A pdb=" N LEU B 326 " --> pdb=" O PRO B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 86 through 101 removed outlier: 3.605A pdb=" N SER D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 Processing helix chain 'D' and resid 120 through 140 removed outlier: 3.507A pdb=" N GLN D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER D 130 " --> pdb=" O GLN D 126 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D 140 " --> pdb=" O GLN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 163 Processing helix chain 'D' and resid 165 through 186 removed outlier: 3.606A pdb=" N ARG D 170 " --> pdb=" O PRO D 166 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 212 removed outlier: 4.269A pdb=" N SER D 212 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 226 removed outlier: 3.931A pdb=" N SER D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG D 224 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 241 Processing helix chain 'D' and resid 242 through 246 Processing helix chain 'D' and resid 249 through 279 removed outlier: 5.337A pdb=" N LYS D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS D 256 " --> pdb=" O GLN D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 327 Processing helix chain 'D' and resid 337 through 350 removed outlier: 3.580A pdb=" N ILE D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 388 Proline residue: D 370 - end of helix Processing helix chain 'D' and resid 389 through 393 removed outlier: 4.335A pdb=" N ARG D 393 " --> pdb=" O ARG D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 409 Proline residue: D 403 - end of helix Processing helix chain 'D' and resid 424 through 443 Processing helix chain 'D' and resid 444 through 446 No H-bonds generated for 'chain 'D' and resid 444 through 446' Processing helix chain 'D' and resid 451 through 467 removed outlier: 4.229A pdb=" N GLY D 455 " --> pdb=" O GLY D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 537 Processing helix chain 'D' and resid 541 through 561 Proline residue: D 554 - end of helix removed outlier: 4.065A pdb=" N GLN D 560 " --> pdb=" O VAL D 556 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN D 561 " --> pdb=" O MET D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 571 Processing helix chain 'D' and resid 572 through 589 Processing helix chain 'D' and resid 597 through 609 Processing helix chain 'D' and resid 613 through 632 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 34 removed outlier: 6.952A pdb=" N ASN A 30 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU A 24 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 47 removed outlier: 5.844A pdb=" N ALA A 55 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N ARG A 42 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 10.017A pdb=" N LEU A 53 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N LEU A 44 " --> pdb=" O TYR A 51 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N TYR A 51 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR A 61 " --> pdb=" O GLN A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.609A pdb=" N VAL A 115 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU A 107 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 113 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 180 removed outlier: 3.557A pdb=" N ASP A 177 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU A 202 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 208 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 223 Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 277 removed outlier: 3.909A pdb=" N THR A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 293 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR A 306 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 295 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 302 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 396 through 398 Processing sheet with id=AA9, first strand: chain 'B' and resid 30 through 34 removed outlier: 6.951A pdb=" N ASN B 30 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU B 24 " --> pdb=" O ASN B 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 39 through 47 removed outlier: 5.844A pdb=" N ALA B 55 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N ARG B 42 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 10.019A pdb=" N LEU B 53 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N LEU B 44 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 11.293A pdb=" N TYR B 51 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR B 61 " --> pdb=" O GLN B 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.611A pdb=" N VAL B 115 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU B 107 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 113 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 124 through 129 Processing sheet with id=AB4, first strand: chain 'B' and resid 175 through 180 removed outlier: 3.556A pdb=" N ASP B 177 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU B 202 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU B 208 " --> pdb=" O GLU B 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 218 through 223 Processing sheet with id=AB6, first strand: chain 'B' and resid 272 through 277 removed outlier: 3.909A pdb=" N THR B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 293 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 306 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 295 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 302 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 396 through 398 782 hydrogen bonds defined for protein. 2256 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: 2.15 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4330 1.34 - 1.46: 2720 1.46 - 1.58: 6254 1.58 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 13430 Sorted by residual: bond pdb=" SD MET D 70 " pdb=" CE MET D 70 " ideal model delta sigma weight residual 1.791 1.756 0.035 2.50e-02 1.60e+03 1.99e+00 bond pdb=" SD MET C 70 " pdb=" CE MET C 70 " ideal model delta sigma weight residual 1.791 1.757 0.034 2.50e-02 1.60e+03 1.89e+00 bond pdb=" CB VAL A 283 " pdb=" CG1 VAL A 283 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.23e+00 bond pdb=" CB VAL B 283 " pdb=" CG1 VAL B 283 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CG LEU B 412 " pdb=" CD1 LEU B 412 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 ... (remaining 13425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 17639 1.49 - 2.97: 486 2.97 - 4.46: 95 4.46 - 5.94: 28 5.94 - 7.43: 4 Bond angle restraints: 18252 Sorted by residual: angle pdb=" C LEU A 412 " pdb=" N ARG A 413 " pdb=" CA ARG A 413 " ideal model delta sigma weight residual 121.14 116.41 4.73 1.75e+00 3.27e-01 7.30e+00 angle pdb=" C LEU B 412 " pdb=" N ARG B 413 " pdb=" CA ARG B 413 " ideal model delta sigma weight residual 121.14 116.42 4.72 1.75e+00 3.27e-01 7.29e+00 angle pdb=" C LEU C 534 " pdb=" N MET C 535 " pdb=" CA MET C 535 " ideal model delta sigma weight residual 121.92 117.87 4.05 1.73e+00 3.34e-01 5.47e+00 angle pdb=" C LEU D 534 " pdb=" N MET D 535 " pdb=" CA MET D 535 " ideal model delta sigma weight residual 121.92 117.90 4.02 1.73e+00 3.34e-01 5.41e+00 angle pdb=" N ARG B 413 " pdb=" CA ARG B 413 " pdb=" CB ARG B 413 " ideal model delta sigma weight residual 110.40 114.03 -3.63 1.63e+00 3.76e-01 4.97e+00 ... (remaining 18247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 7446 16.24 - 32.47: 522 32.47 - 48.71: 88 48.71 - 64.94: 18 64.94 - 81.18: 14 Dihedral angle restraints: 8088 sinusoidal: 3070 harmonic: 5018 Sorted by residual: dihedral pdb=" CA TRP A 65 " pdb=" C TRP A 65 " pdb=" N GLU A 66 " pdb=" CA GLU A 66 " ideal model delta harmonic sigma weight residual 180.00 164.37 15.63 0 5.00e+00 4.00e-02 9.77e+00 dihedral pdb=" CA TRP B 65 " pdb=" C TRP B 65 " pdb=" N GLU B 66 " pdb=" CA GLU B 66 " ideal model delta harmonic sigma weight residual 180.00 164.40 15.60 0 5.00e+00 4.00e-02 9.74e+00 dihedral pdb=" CA SER D 519 " pdb=" C SER D 519 " pdb=" N ASP D 520 " pdb=" CA ASP D 520 " ideal model delta harmonic sigma weight residual 180.00 -164.46 -15.54 0 5.00e+00 4.00e-02 9.65e+00 ... (remaining 8085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1617 0.041 - 0.082: 389 0.082 - 0.122: 154 0.122 - 0.163: 19 0.163 - 0.204: 3 Chirality restraints: 2182 Sorted by residual: chirality pdb=" CG LEU D 37 " pdb=" CB LEU D 37 " pdb=" CD1 LEU D 37 " pdb=" CD2 LEU D 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CG LEU C 37 " pdb=" CB LEU C 37 " pdb=" CD1 LEU C 37 " pdb=" CD2 LEU C 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CA ARG B 413 " pdb=" N ARG B 413 " pdb=" C ARG B 413 " pdb=" CB ARG B 413 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 2179 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 165 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO D 166 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 166 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 166 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 165 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO C 166 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 166 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 166 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 173 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C SER D 173 " 0.034 2.00e-02 2.50e+03 pdb=" O SER D 173 " -0.013 2.00e-02 2.50e+03 pdb=" N MET D 174 " -0.012 2.00e-02 2.50e+03 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 160 2.68 - 3.24: 12733 3.24 - 3.79: 21540 3.79 - 4.35: 29247 4.35 - 4.90: 48540 Nonbonded interactions: 112220 Sorted by model distance: nonbonded pdb=" OH TYR D 432 " pdb=" OD2 ASP D 465 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR C 432 " pdb=" OD2 ASP C 465 " model vdw 2.127 3.040 nonbonded pdb=" O LEU D 115 " pdb=" OG SER D 119 " model vdw 2.145 3.040 nonbonded pdb=" O LEU C 115 " pdb=" OG SER C 119 " model vdw 2.145 3.040 nonbonded pdb=" O LEU D 38 " pdb=" OG SER D 42 " model vdw 2.277 3.040 ... (remaining 112215 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.150 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13430 Z= 0.154 Angle : 0.617 7.430 18252 Z= 0.310 Chirality : 0.043 0.204 2182 Planarity : 0.005 0.064 2310 Dihedral : 12.055 81.179 4832 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.21), residues: 1708 helix: 2.14 (0.18), residues: 816 sheet: 0.32 (0.30), residues: 278 loop : -0.27 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 577 TYR 0.017 0.002 TYR D 240 PHE 0.026 0.002 PHE D 619 TRP 0.013 0.002 TRP A 201 HIS 0.005 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00353 (13430) covalent geometry : angle 0.61711 (18252) hydrogen bonds : bond 0.13799 ( 782) hydrogen bonds : angle 5.69216 ( 2256) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.513 Fit side-chains REVERT: C 520 ASP cc_start: 0.6601 (t0) cc_final: 0.6285 (t0) REVERT: C 535 MET cc_start: 0.8255 (mmm) cc_final: 0.7904 (mmm) REVERT: B 310 LYS cc_start: 0.8368 (mmtm) cc_final: 0.7984 (mptt) REVERT: B 325 MET cc_start: 0.8491 (mtt) cc_final: 0.8254 (mtt) REVERT: D 70 MET cc_start: 0.7211 (mmm) cc_final: 0.6946 (tpt) REVERT: D 240 TYR cc_start: 0.8259 (t80) cc_final: 0.8058 (t80) REVERT: D 308 LEU cc_start: 0.8375 (mt) cc_final: 0.8164 (tp) REVERT: D 535 MET cc_start: 0.8216 (mmm) cc_final: 0.7901 (mmm) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.7384 time to fit residues: 193.5832 Evaluate side-chains 197 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN D 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.160641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.130676 restraints weight = 13441.754| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.34 r_work: 0.3228 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13430 Z= 0.170 Angle : 0.617 9.961 18252 Z= 0.312 Chirality : 0.043 0.174 2182 Planarity : 0.005 0.050 2310 Dihedral : 4.236 15.989 1856 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.94 % Allowed : 8.32 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.21), residues: 1708 helix: 2.55 (0.18), residues: 818 sheet: 0.55 (0.31), residues: 278 loop : -0.44 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 133 TYR 0.012 0.002 TYR A 121 PHE 0.020 0.002 PHE B 136 TRP 0.014 0.002 TRP B 201 HIS 0.005 0.001 HIS B 179 Details of bonding type rmsd covalent geometry : bond 0.00393 (13430) covalent geometry : angle 0.61718 (18252) hydrogen bonds : bond 0.04846 ( 782) hydrogen bonds : angle 4.72090 ( 2256) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.510 Fit side-chains REVERT: A 305 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7902 (ttm-80) REVERT: C 70 MET cc_start: 0.7164 (mmm) cc_final: 0.6926 (mmm) REVERT: C 188 ARG cc_start: 0.6914 (mtm-85) cc_final: 0.6394 (mtm-85) REVERT: C 197 GLU cc_start: 0.7942 (mp0) cc_final: 0.7670 (mt-10) REVERT: C 593 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7166 (ptt-90) REVERT: B 72 GLN cc_start: 0.5852 (tp40) cc_final: 0.5296 (tp40) REVERT: B 263 LYS cc_start: 0.8603 (mmtm) cc_final: 0.8296 (mmtp) REVERT: B 282 SER cc_start: 0.8857 (p) cc_final: 0.8636 (p) REVERT: B 305 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7402 (ttp80) REVERT: B 310 LYS cc_start: 0.8421 (mmtm) cc_final: 0.8084 (mptt) REVERT: B 325 MET cc_start: 0.8596 (mtt) cc_final: 0.8329 (mtt) REVERT: D 197 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: D 262 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7946 (mp10) REVERT: D 577 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8032 (ttp80) outliers start: 28 outliers final: 9 residues processed: 226 average time/residue: 0.7464 time to fit residues: 180.3750 Evaluate side-chains 223 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 305 ARG Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 577 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 69 optimal weight: 2.9990 chunk 111 optimal weight: 0.0980 chunk 146 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 80 optimal weight: 0.0970 chunk 36 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN C 373 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN D 560 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.158612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.128581 restraints weight = 13558.213| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.37 r_work: 0.3189 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13430 Z= 0.186 Angle : 0.638 10.163 18252 Z= 0.317 Chirality : 0.044 0.199 2182 Planarity : 0.005 0.046 2310 Dihedral : 4.371 17.184 1856 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.84 % Allowed : 11.37 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.20), residues: 1708 helix: 2.52 (0.18), residues: 820 sheet: 0.50 (0.31), residues: 282 loop : -0.49 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 133 TYR 0.010 0.002 TYR C 240 PHE 0.020 0.002 PHE B 136 TRP 0.012 0.002 TRP B 201 HIS 0.005 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00438 (13430) covalent geometry : angle 0.63756 (18252) hydrogen bonds : bond 0.04794 ( 782) hydrogen bonds : angle 4.73040 ( 2256) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.518 Fit side-chains REVERT: A 72 GLN cc_start: 0.5777 (tp40) cc_final: 0.5315 (tp40) REVERT: C 170 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6403 (ptp90) REVERT: C 174 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6589 (mpp) REVERT: C 188 ARG cc_start: 0.7021 (mtm-85) cc_final: 0.6521 (mtm-85) REVERT: C 262 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: C 593 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7041 (ptt-90) REVERT: B 72 GLN cc_start: 0.5935 (tp40) cc_final: 0.5414 (tp40) REVERT: B 305 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7278 (ttp80) REVERT: B 310 LYS cc_start: 0.8477 (mmtm) cc_final: 0.8150 (mptt) REVERT: B 325 MET cc_start: 0.8743 (mtt) cc_final: 0.8486 (mtt) REVERT: D 174 MET cc_start: 0.6895 (mtt) cc_final: 0.6583 (mmt) REVERT: D 197 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: D 262 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7935 (mp10) REVERT: D 577 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8051 (ttp80) outliers start: 41 outliers final: 13 residues processed: 228 average time/residue: 0.7393 time to fit residues: 180.1713 Evaluate side-chains 228 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 577 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 37 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS D 560 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.159489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.129605 restraints weight = 13528.373| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.32 r_work: 0.3215 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13430 Z= 0.152 Angle : 0.590 8.739 18252 Z= 0.295 Chirality : 0.042 0.195 2182 Planarity : 0.005 0.044 2310 Dihedral : 4.266 16.866 1856 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.94 % Allowed : 13.87 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.20), residues: 1708 helix: 2.67 (0.18), residues: 820 sheet: 0.56 (0.30), residues: 282 loop : -0.47 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 133 TYR 0.013 0.002 TYR B 61 PHE 0.019 0.002 PHE A 136 TRP 0.015 0.002 TRP B 201 HIS 0.004 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00353 (13430) covalent geometry : angle 0.58973 (18252) hydrogen bonds : bond 0.04343 ( 782) hydrogen bonds : angle 4.61567 ( 2256) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.593 Fit side-chains REVERT: A 72 GLN cc_start: 0.5761 (tp40) cc_final: 0.5354 (tp40) REVERT: C 174 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6707 (mmt) REVERT: C 188 ARG cc_start: 0.6961 (mtm-85) cc_final: 0.6479 (mtm-85) REVERT: C 262 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7979 (mp10) REVERT: C 593 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7068 (ptt-90) REVERT: C 630 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7941 (mt) REVERT: B 72 GLN cc_start: 0.5703 (tp40) cc_final: 0.5171 (tp40) REVERT: B 207 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: B 295 LEU cc_start: 0.9108 (mt) cc_final: 0.8835 (mm) REVERT: B 325 MET cc_start: 0.8718 (mtt) cc_final: 0.8482 (mtt) REVERT: D 197 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: D 262 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7973 (mp10) REVERT: D 577 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7974 (ttp80) REVERT: D 593 ARG cc_start: 0.7419 (ptp90) cc_final: 0.7167 (ptt90) REVERT: D 630 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7981 (mt) outliers start: 28 outliers final: 7 residues processed: 226 average time/residue: 0.7208 time to fit residues: 174.6724 Evaluate side-chains 219 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 577 ARG Chi-restraints excluded: chain D residue 630 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 155 optimal weight: 0.1980 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN C 65 HIS B 30 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 560 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.160513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.130519 restraints weight = 13427.042| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.35 r_work: 0.3222 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13430 Z= 0.132 Angle : 0.569 8.598 18252 Z= 0.284 Chirality : 0.041 0.204 2182 Planarity : 0.005 0.043 2310 Dihedral : 4.160 16.310 1856 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.87 % Allowed : 15.05 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.21), residues: 1708 helix: 2.80 (0.18), residues: 820 sheet: 0.65 (0.31), residues: 278 loop : -0.47 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 133 TYR 0.013 0.001 TYR B 61 PHE 0.018 0.002 PHE A 136 TRP 0.016 0.002 TRP B 201 HIS 0.004 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00305 (13430) covalent geometry : angle 0.56906 (18252) hydrogen bonds : bond 0.04079 ( 782) hydrogen bonds : angle 4.52486 ( 2256) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.423 Fit side-chains REVERT: A 17 MET cc_start: 0.8593 (ptt) cc_final: 0.8372 (ptt) REVERT: A 72 GLN cc_start: 0.5793 (tp40) cc_final: 0.5343 (tp40) REVERT: C 174 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6589 (mmt) REVERT: C 188 ARG cc_start: 0.6934 (mtm-85) cc_final: 0.6447 (mtm-85) REVERT: C 262 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7983 (mp10) REVERT: C 593 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7010 (ptt-90) REVERT: B 72 GLN cc_start: 0.5785 (tp40) cc_final: 0.5300 (tp40) REVERT: B 207 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: B 295 LEU cc_start: 0.9041 (mt) cc_final: 0.8807 (mm) REVERT: B 325 MET cc_start: 0.8713 (mtt) cc_final: 0.8481 (mtt) REVERT: D 197 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: D 262 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: D 577 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8020 (ttp80) outliers start: 27 outliers final: 9 residues processed: 224 average time/residue: 0.7126 time to fit residues: 171.1584 Evaluate side-chains 224 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 577 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 14 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 103 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN C 65 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.160068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.130045 restraints weight = 13491.767| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.36 r_work: 0.3225 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13430 Z= 0.139 Angle : 0.581 8.878 18252 Z= 0.289 Chirality : 0.041 0.206 2182 Planarity : 0.005 0.043 2310 Dihedral : 4.159 16.308 1856 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.15 % Allowed : 14.91 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.21), residues: 1708 helix: 2.78 (0.18), residues: 820 sheet: 0.67 (0.31), residues: 278 loop : -0.44 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 133 TYR 0.010 0.001 TYR B 121 PHE 0.018 0.002 PHE A 136 TRP 0.014 0.002 TRP B 201 HIS 0.004 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00324 (13430) covalent geometry : angle 0.58065 (18252) hydrogen bonds : bond 0.04128 ( 782) hydrogen bonds : angle 4.51886 ( 2256) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 0.345 Fit side-chains REVERT: A 17 MET cc_start: 0.8589 (ptt) cc_final: 0.8355 (ptt) REVERT: A 72 GLN cc_start: 0.5673 (tp40) cc_final: 0.5229 (tp40) REVERT: C 188 ARG cc_start: 0.6953 (mtm-85) cc_final: 0.6474 (mtm-85) REVERT: C 262 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: C 593 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7046 (ptt-90) REVERT: B 72 GLN cc_start: 0.5731 (tp40) cc_final: 0.5267 (tp40) REVERT: B 207 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: B 295 LEU cc_start: 0.9043 (mt) cc_final: 0.8802 (mm) REVERT: B 325 MET cc_start: 0.8714 (mtt) cc_final: 0.8460 (mtt) REVERT: D 174 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6454 (mtm) REVERT: D 197 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: D 262 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7978 (mp10) REVERT: D 577 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7974 (ttp80) REVERT: D 593 ARG cc_start: 0.7457 (ptp90) cc_final: 0.7193 (ptt90) REVERT: D 630 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7947 (mt) outliers start: 31 outliers final: 9 residues processed: 224 average time/residue: 0.7150 time to fit residues: 171.8390 Evaluate side-chains 216 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 577 ARG Chi-restraints excluded: chain D residue 630 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 63 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 53 optimal weight: 0.0570 chunk 81 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.158359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.128373 restraints weight = 13429.779| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.31 r_work: 0.3203 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.004 0.041 13430 Z= 0.181 Angle : 0.631 9.382 18252 Z= 0.314 Chirality : 0.043 0.197 2182 Planarity : 0.005 0.044 2310 Dihedral : 4.342 17.515 1856 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.50 % Allowed : 14.84 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.20), residues: 1708 helix: 2.61 (0.18), residues: 820 sheet: 0.65 (0.31), residues: 278 loop : -0.45 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 133 TYR 0.015 0.002 TYR A 61 PHE 0.020 0.002 PHE B 136 TRP 0.012 0.002 TRP A 201 HIS 0.005 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00429 (13430) covalent geometry : angle 0.63140 (18252) hydrogen bonds : bond 0.04561 ( 782) hydrogen bonds : angle 4.64047 ( 2256) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.302 Fit side-chains REVERT: A 72 GLN cc_start: 0.5540 (tp40) cc_final: 0.5116 (tp40) REVERT: C 174 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6807 (mmt) REVERT: C 188 ARG cc_start: 0.6915 (mtm-85) cc_final: 0.6427 (mtm-85) REVERT: C 262 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: C 593 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7044 (ptt-90) REVERT: C 630 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8087 (mt) REVERT: B 238 SER cc_start: 0.8651 (p) cc_final: 0.8361 (m) REVERT: B 295 LEU cc_start: 0.9060 (mt) cc_final: 0.8842 (mm) REVERT: D 70 MET cc_start: 0.6905 (mmm) cc_final: 0.6703 (mmm) REVERT: D 174 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6557 (mtm) REVERT: D 197 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: D 262 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7955 (mp10) REVERT: D 560 GLN cc_start: 0.7310 (mm-40) cc_final: 0.6368 (mt0) REVERT: D 577 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7959 (ttp80) REVERT: D 630 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8031 (mt) outliers start: 36 outliers final: 15 residues processed: 221 average time/residue: 0.7089 time to fit residues: 167.8286 Evaluate side-chains 225 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 577 ARG Chi-restraints excluded: chain D residue 630 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 114 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 110 optimal weight: 0.0170 chunk 160 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** 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 = 0.3752 r_free = 0.3752 target = 0.160881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.131192 restraints weight = 13401.229| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.25 r_work: 0.3243 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13430 Z= 0.122 Angle : 0.571 8.598 18252 Z= 0.285 Chirality : 0.041 0.194 2182 Planarity : 0.005 0.043 2310 Dihedral : 4.147 17.139 1856 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.60 % Allowed : 15.74 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.21), residues: 1708 helix: 2.78 (0.18), residues: 820 sheet: 0.72 (0.31), residues: 278 loop : -0.41 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 133 TYR 0.015 0.001 TYR A 61 PHE 0.017 0.002 PHE A 136 TRP 0.018 0.002 TRP B 201 HIS 0.004 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00278 (13430) covalent geometry : angle 0.57105 (18252) hydrogen bonds : bond 0.03911 ( 782) hydrogen bonds : angle 4.43782 ( 2256) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.464 Fit side-chains REVERT: A 17 MET cc_start: 0.8555 (ptt) cc_final: 0.8331 (ptt) REVERT: C 174 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6638 (mmt) REVERT: C 188 ARG cc_start: 0.6861 (mtm-85) cc_final: 0.6400 (mtm-85) REVERT: C 262 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: C 593 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7069 (ptt-90) REVERT: B 207 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: B 295 LEU cc_start: 0.9016 (mt) cc_final: 0.8800 (mm) REVERT: D 174 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.6449 (mtm) REVERT: D 197 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: D 262 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7989 (mp10) REVERT: D 560 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6350 (mt0) REVERT: D 577 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8009 (ttp80) outliers start: 23 outliers final: 8 residues processed: 216 average time/residue: 0.7429 time to fit residues: 172.3872 Evaluate side-chains 215 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 577 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 89 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 75 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 144 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.161167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.131197 restraints weight = 13522.047| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.35 r_work: 0.3233 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13430 Z= 0.125 Angle : 0.584 8.872 18252 Z= 0.290 Chirality : 0.041 0.214 2182 Planarity : 0.005 0.043 2310 Dihedral : 4.105 17.157 1856 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.60 % Allowed : 16.09 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.21), residues: 1708 helix: 2.81 (0.18), residues: 820 sheet: 0.70 (0.31), residues: 280 loop : -0.37 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 133 TYR 0.015 0.002 TYR A 61 PHE 0.018 0.002 PHE A 420 TRP 0.016 0.002 TRP A 201 HIS 0.004 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00288 (13430) covalent geometry : angle 0.58420 (18252) hydrogen bonds : bond 0.03915 ( 782) hydrogen bonds : angle 4.41813 ( 2256) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 0.350 Fit side-chains REVERT: A 207 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: C 174 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6648 (mmt) REVERT: C 188 ARG cc_start: 0.6862 (mtm-85) cc_final: 0.6392 (mtm-85) REVERT: C 262 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: C 593 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6976 (ptt-90) REVERT: C 630 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7946 (mt) REVERT: B 207 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: B 295 LEU cc_start: 0.9019 (mt) cc_final: 0.8806 (mm) REVERT: D 107 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7345 (mp0) REVERT: D 174 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.6447 (mtm) REVERT: D 197 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: D 262 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: D 520 ASP cc_start: 0.8855 (m-30) cc_final: 0.8638 (m-30) REVERT: D 560 GLN cc_start: 0.7019 (mm-40) cc_final: 0.6479 (mt0) REVERT: D 577 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8025 (ttp80) outliers start: 23 outliers final: 8 residues processed: 209 average time/residue: 0.7233 time to fit residues: 162.3163 Evaluate side-chains 214 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 577 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 57 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.156696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.126879 restraints weight = 13544.903| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.26 r_work: 0.3188 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13430 Z= 0.257 Angle : 0.717 10.464 18252 Z= 0.355 Chirality : 0.047 0.177 2182 Planarity : 0.006 0.044 2310 Dihedral : 4.534 18.064 1856 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.66 % Allowed : 16.23 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.20), residues: 1708 helix: 2.38 (0.18), residues: 822 sheet: 0.46 (0.30), residues: 284 loop : -0.37 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 133 TYR 0.020 0.003 TYR A 61 PHE 0.025 0.003 PHE B 420 TRP 0.009 0.002 TRP A 201 HIS 0.008 0.002 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00611 (13430) covalent geometry : angle 0.71721 (18252) hydrogen bonds : bond 0.05109 ( 782) hydrogen bonds : angle 4.80390 ( 2256) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.518 Fit side-chains REVERT: C 70 MET cc_start: 0.6671 (mmm) cc_final: 0.6374 (tpt) REVERT: C 262 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: C 593 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7090 (ptt-90) REVERT: C 630 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8091 (mt) REVERT: B 238 SER cc_start: 0.8644 (p) cc_final: 0.8237 (m) REVERT: D 107 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7365 (mp0) REVERT: D 174 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6629 (mtm) REVERT: D 197 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: D 262 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7983 (mp10) REVERT: D 520 ASP cc_start: 0.8901 (m-30) cc_final: 0.8666 (m-30) REVERT: D 577 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8004 (ttp80) outliers start: 24 outliers final: 10 residues processed: 211 average time/residue: 0.7339 time to fit residues: 166.2857 Evaluate side-chains 216 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 577 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 146 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS C 310 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS D 164 GLN D 560 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.158994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.129369 restraints weight = 13475.990| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.32 r_work: 0.3204 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13430 Z= 0.159 Angle : 0.621 8.926 18252 Z= 0.310 Chirality : 0.042 0.184 2182 Planarity : 0.005 0.044 2310 Dihedral : 4.356 16.981 1856 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.80 % Allowed : 16.50 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.21), residues: 1708 helix: 2.57 (0.18), residues: 820 sheet: 0.56 (0.31), residues: 280 loop : -0.42 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 133 TYR 0.018 0.002 TYR A 61 PHE 0.021 0.002 PHE B 136 TRP 0.014 0.002 TRP B 201 HIS 0.004 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00374 (13430) covalent geometry : angle 0.62086 (18252) hydrogen bonds : bond 0.04361 ( 782) hydrogen bonds : angle 4.63690 ( 2256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4814.19 seconds wall clock time: 82 minutes 36.74 seconds (4956.74 seconds total)