Starting phenix.real_space_refine on Mon Apr 6 09:16:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e5n_47527/04_2026/9e5n_47527.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e5n_47527/04_2026/9e5n_47527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e5n_47527/04_2026/9e5n_47527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e5n_47527/04_2026/9e5n_47527.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e5n_47527/04_2026/9e5n_47527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e5n_47527/04_2026/9e5n_47527.map" } resolution = 2.2 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= 0.060 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 90 5.16 5 C 10614 2.51 5 N 2925 2.21 5 O 3363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16992 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5559 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 29, 'TRANS': 669} Chain breaks: 5 Chain: "B" Number of atoms: 5559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5559 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 29, 'TRANS': 669} Chain breaks: 5 Chain: "C" Number of atoms: 5559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5559 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 29, 'TRANS': 669} Chain breaks: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Time building chain proxies: 3.98, per 1000 atoms: 0.23 Number of scatterers: 16992 At special positions: 0 Unit cell: (122.1, 115.5, 184.14, 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 90 16.00 O 3363 8.00 N 2925 7.00 C 10614 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.04 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.04 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.04 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.04 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.04 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.04 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.04 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.04 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.04 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.04 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 141 " " NAG A1002 " - " ASN A 398 " " NAG B1001 " - " ASN B 141 " " NAG B1002 " - " ASN B 398 " " NAG C1001 " - " ASN C 141 " " NAG C1002 " - " ASN C 398 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 711.9 milliseconds 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3930 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 24 sheets defined 35.6% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 91 through 106 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.710A pdb=" N ILE A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 306 through 310 removed outlier: 4.056A pdb=" N THR A 309 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 429 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 510 through 546 removed outlier: 3.854A pdb=" N HIS A 516 " --> pdb=" O HIS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 701 through 724 Processing helix chain 'A' and resid 728 through 739 Processing helix chain 'A' and resid 747 through 772 Processing helix chain 'A' and resid 773 through 803 removed outlier: 3.592A pdb=" N SER A 803 " --> pdb=" O MET A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 810 Processing helix chain 'A' and resid 836 through 865 removed outlier: 3.607A pdb=" N TYR A 849 " --> pdb=" O GLU A 845 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 853 " --> pdb=" O TYR A 849 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 854 " --> pdb=" O MET A 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 106 Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.730A pdb=" N ILE B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 306 through 310 removed outlier: 4.074A pdb=" N THR B 309 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 429 Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 510 through 546 removed outlier: 3.885A pdb=" N HIS B 516 " --> pdb=" O HIS B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 701 through 724 Processing helix chain 'B' and resid 728 through 739 Processing helix chain 'B' and resid 747 through 772 Processing helix chain 'B' and resid 773 through 803 removed outlier: 3.631A pdb=" N SER B 803 " --> pdb=" O MET B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 810 Processing helix chain 'B' and resid 836 through 865 removed outlier: 3.548A pdb=" N ARG B 848 " --> pdb=" O ARG B 844 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B 851 " --> pdb=" O ILE B 847 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU B 852 " --> pdb=" O ARG B 848 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL B 853 " --> pdb=" O TYR B 849 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 854 " --> pdb=" O MET B 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 106 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.739A pdb=" N ILE C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 306 through 310 removed outlier: 4.045A pdb=" N THR C 309 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 429 Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 510 through 546 removed outlier: 3.882A pdb=" N HIS C 516 " --> pdb=" O HIS C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 686 through 691 Processing helix chain 'C' and resid 701 through 725 removed outlier: 3.555A pdb=" N ALA C 725 " --> pdb=" O THR C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 739 Processing helix chain 'C' and resid 747 through 772 Processing helix chain 'C' and resid 773 through 803 removed outlier: 3.647A pdb=" N SER C 803 " --> pdb=" O MET C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 810 Processing helix chain 'C' and resid 836 through 865 removed outlier: 4.207A pdb=" N ALA C 851 " --> pdb=" O ILE C 847 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU C 852 " --> pdb=" O ARG C 848 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 853 " --> pdb=" O TYR C 849 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 854 " --> pdb=" O MET C 850 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 6.426A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 563 removed outlier: 4.163A pdb=" N THR B 665 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 433 through 435 removed outlier: 3.525A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU A 443 " --> pdb=" O ASN A 398 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN A 398 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU A 374 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY A 145 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU A 376 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR A 143 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER A 378 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN A 141 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 14.101A pdb=" N TYR A 142 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N SER A 457 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 191 Processing sheet with id=AA5, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.242A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 210 through 213 Processing sheet with id=AA7, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AA8, first strand: chain 'A' and resid 638 through 643 removed outlier: 3.546A pdb=" N HIS A 657 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 665 through 667 removed outlier: 6.500A pdb=" N THR A 665 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.413A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 559 through 563 removed outlier: 4.161A pdb=" N THR C 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 433 through 435 removed outlier: 6.277A pdb=" N LEU B 443 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN B 398 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP B 369 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LYS B 151 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU B 371 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B 149 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASP B 373 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA B 147 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU B 379 " --> pdb=" O ASN B 141 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASN B 141 " --> pdb=" O GLU B 379 " (cutoff:3.500A) removed outlier: 13.915A pdb=" N TYR B 142 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N SER B 457 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 186 through 191 Processing sheet with id=AB5, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.292A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 210 through 213 Processing sheet with id=AB7, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AB8, first strand: chain 'B' and resid 638 through 643 removed outlier: 3.562A pdb=" N HIS B 657 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.427A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 433 through 435 removed outlier: 3.570A pdb=" N PHE C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU C 443 " --> pdb=" O ASN C 398 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN C 398 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N THR C 367 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU C 152 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TRP C 369 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE C 150 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU C 371 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL C 148 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ASP C 373 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE C 146 " --> pdb=" O ASP C 373 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET C 375 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU C 144 " --> pdb=" O MET C 375 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG C 377 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR C 142 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 13.922A pdb=" N TYR C 142 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N SER C 457 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 186 through 191 Processing sheet with id=AC3, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.267A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 210 through 213 Processing sheet with id=AC5, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AC6, first strand: chain 'C' and resid 638 through 643 removed outlier: 3.528A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) 878 hydrogen bonds defined for protein. 2484 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: 3.47 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5533 1.34 - 1.46: 4048 1.46 - 1.58: 7420 1.58 - 1.71: 0 1.71 - 1.83: 150 Bond restraints: 17151 Sorted by residual: bond pdb=" N VAL B 635 " pdb=" CA VAL B 635 " ideal model delta sigma weight residual 1.459 1.509 -0.050 9.10e-03 1.21e+04 3.02e+01 bond pdb=" N VAL A 559 " pdb=" CA VAL A 559 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.19e+01 bond pdb=" N CYS A 633 " pdb=" CA CYS A 633 " ideal model delta sigma weight residual 1.455 1.497 -0.042 1.27e-02 6.20e+03 1.12e+01 bond pdb=" N CYS C 633 " pdb=" CA CYS C 633 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" N CYS C 133 " pdb=" CA CYS C 133 " ideal model delta sigma weight residual 1.460 1.418 0.042 1.29e-02 6.01e+03 1.06e+01 ... (remaining 17146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 22332 1.56 - 3.12: 779 3.12 - 4.68: 122 4.68 - 6.23: 11 6.23 - 7.79: 9 Bond angle restraints: 23253 Sorted by residual: angle pdb=" C ARG C 132 " pdb=" N CYS C 133 " pdb=" CA CYS C 133 " ideal model delta sigma weight residual 122.56 115.42 7.14 1.34e+00 5.57e-01 2.84e+01 angle pdb=" CA THR C 634 " pdb=" C THR C 634 " pdb=" O THR C 634 " ideal model delta sigma weight residual 121.49 115.50 5.99 1.16e+00 7.43e-01 2.67e+01 angle pdb=" CA THR A 634 " pdb=" C THR A 634 " pdb=" O THR A 634 " ideal model delta sigma weight residual 121.49 115.70 5.79 1.16e+00 7.43e-01 2.49e+01 angle pdb=" CA THR B 634 " pdb=" C THR B 634 " pdb=" O THR B 634 " ideal model delta sigma weight residual 121.60 116.80 4.80 1.21e+00 6.83e-01 1.57e+01 angle pdb=" N GLN A 507 " pdb=" CA GLN A 507 " pdb=" C GLN A 507 " ideal model delta sigma weight residual 109.46 103.00 6.46 1.66e+00 3.63e-01 1.51e+01 ... (remaining 23248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 8944 17.46 - 34.92: 979 34.92 - 52.38: 251 52.38 - 69.84: 83 69.84 - 87.30: 15 Dihedral angle restraints: 10272 sinusoidal: 4158 harmonic: 6114 Sorted by residual: dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 529 " pdb=" CB CYS B 529 " ideal model delta sinusoidal sigma weight residual -86.00 -173.30 87.30 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS C 133 " pdb=" SG CYS C 133 " pdb=" SG CYS C 529 " pdb=" CB CYS C 529 " ideal model delta sinusoidal sigma weight residual -86.00 -169.64 83.64 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 529 " pdb=" CB CYS A 529 " ideal model delta sinusoidal sigma weight residual -86.00 -168.00 82.00 1 1.00e+01 1.00e-02 8.26e+01 ... (remaining 10269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1927 0.046 - 0.091: 462 0.091 - 0.137: 143 0.137 - 0.183: 12 0.183 - 0.228: 9 Chirality restraints: 2553 Sorted by residual: chirality pdb=" CA ILE A 185 " pdb=" N ILE A 185 " pdb=" C ILE A 185 " pdb=" CB ILE A 185 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 141 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE B 513 " pdb=" N ILE B 513 " pdb=" C ILE B 513 " pdb=" CB ILE B 513 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2550 not shown) Planarity restraints: 3024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1002 " -0.060 2.00e-02 2.50e+03 4.91e-02 3.02e+01 pdb=" C7 NAG C1002 " 0.017 2.00e-02 2.50e+03 pdb=" C8 NAG C1002 " -0.045 2.00e-02 2.50e+03 pdb=" N2 NAG C1002 " 0.078 2.00e-02 2.50e+03 pdb=" O7 NAG C1002 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 557 " -0.241 9.50e-02 1.11e+02 1.08e-01 7.16e+00 pdb=" NE ARG A 557 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 557 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 557 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 557 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 137 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C PRO A 137 " 0.036 2.00e-02 2.50e+03 pdb=" O PRO A 137 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 138 " -0.012 2.00e-02 2.50e+03 ... (remaining 3021 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1503 2.75 - 3.29: 16056 3.29 - 3.82: 29022 3.82 - 4.36: 34272 4.36 - 4.90: 57250 Nonbonded interactions: 138103 Sorted by model distance: nonbonded pdb=" OG1 THR A 241 " pdb=" OG SER A 244 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR C 241 " pdb=" OG SER C 244 " model vdw 2.210 3.040 nonbonded pdb=" O ASP B 836 " pdb=" OH TYR C 849 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR A 849 " pdb=" O ASP C 836 " model vdw 2.223 3.040 nonbonded pdb=" CG2 THR A 123 " pdb=" O HOH A1141 " model vdw 2.227 3.460 ... (remaining 138098 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' selection = chain 'C' } 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: 11.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 16.350 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 0.050 17169 Z= 0.255 Angle : 0.677 7.793 23295 Z= 0.405 Chirality : 0.046 0.228 2553 Planarity : 0.005 0.108 3018 Dihedral : 16.194 83.043 6306 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.96 % Allowed : 19.91 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.18), residues: 2061 helix: 3.10 (0.19), residues: 678 sheet: 0.65 (0.22), residues: 507 loop : -0.37 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 558 TYR 0.015 0.002 TYR A 301 PHE 0.013 0.002 PHE B 534 TRP 0.017 0.002 TRP C 247 HIS 0.002 0.001 HIS B 433 Details of bonding type rmsd covalent geometry : bond 0.00399 (17151) covalent geometry : angle 0.66802 (23253) SS BOND : bond 0.00798 ( 12) SS BOND : angle 2.55430 ( 24) hydrogen bonds : bond 0.13861 ( 836) hydrogen bonds : angle 6.33681 ( 2484) link_NAG-ASN : bond 0.00485 ( 6) link_NAG-ASN : angle 2.71020 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: A 692 HIS cc_start: 0.7521 (m90) cc_final: 0.7057 (m-70) REVERT: B 232 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.5739 (mmm) REVERT: B 416 ASP cc_start: 0.7329 (m-30) cc_final: 0.6812 (t0) REVERT: B 731 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.5146 (ptp) REVERT: B 846 MET cc_start: 0.4041 (tpp) cc_final: 0.3281 (mtm) REVERT: C 232 MET cc_start: 0.6015 (mpt) cc_final: 0.5756 (mmm) REVERT: C 343 ASN cc_start: 0.7090 (m-40) cc_final: 0.6389 (t0) REVERT: C 541 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: C 731 MET cc_start: 0.5683 (OUTLIER) cc_final: 0.5313 (ptp) REVERT: C 846 MET cc_start: 0.4476 (tpp) cc_final: 0.3587 (mtm) outliers start: 52 outliers final: 36 residues processed: 195 average time/residue: 0.6326 time to fit residues: 136.7702 Evaluate side-chains 193 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 810 TYR Chi-restraints excluded: chain A residue 856 MET Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain B residue 835 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 810 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.0040 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.216941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138390 restraints weight = 13240.967| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.00 r_work: 0.3185 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17169 Z= 0.161 Angle : 0.604 7.189 23295 Z= 0.327 Chirality : 0.044 0.217 2553 Planarity : 0.004 0.039 3018 Dihedral : 8.381 62.523 2544 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.61 % Allowed : 18.32 % Favored : 77.08 % 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: 1.65 (0.18), residues: 2061 helix: 2.95 (0.19), residues: 690 sheet: 0.76 (0.22), residues: 534 loop : -0.26 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 562 TYR 0.014 0.002 TYR B 849 PHE 0.017 0.002 PHE A 287 TRP 0.012 0.002 TRP A 539 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00329 (17151) covalent geometry : angle 0.60044 (23253) SS BOND : bond 0.01159 ( 12) SS BOND : angle 1.48207 ( 24) hydrogen bonds : bond 0.05632 ( 836) hydrogen bonds : angle 4.86708 ( 2484) link_NAG-ASN : bond 0.00103 ( 6) link_NAG-ASN : angle 1.76224 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 153 time to evaluate : 0.652 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: A 187 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7179 (pm20) REVERT: A 214 VAL cc_start: 0.6875 (OUTLIER) cc_final: 0.6567 (t) REVERT: A 232 MET cc_start: 0.6119 (OUTLIER) cc_final: 0.5745 (mmm) REVERT: A 360 ARG cc_start: 0.5801 (OUTLIER) cc_final: 0.5394 (mpp-170) REVERT: A 416 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7184 (m-30) REVERT: A 541 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8383 (mp0) REVERT: A 592 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7247 (ttp-170) REVERT: A 692 HIS cc_start: 0.7819 (m90) cc_final: 0.7401 (m-70) REVERT: A 850 MET cc_start: 0.5733 (tpt) cc_final: 0.5407 (tpt) REVERT: B 187 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7017 (pm20) REVERT: B 214 VAL cc_start: 0.6715 (OUTLIER) cc_final: 0.6487 (t) REVERT: B 360 ARG cc_start: 0.5946 (OUTLIER) cc_final: 0.4059 (mpp-170) REVERT: B 592 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7441 (mtp180) REVERT: B 846 MET cc_start: 0.4087 (tpp) cc_final: 0.3394 (mtm) REVERT: C 167 ASP cc_start: 0.7662 (p0) cc_final: 0.7219 (m-30) REVERT: C 187 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7021 (pm20) REVERT: C 204 LYS cc_start: 0.4690 (OUTLIER) cc_final: 0.4211 (pmtt) REVERT: C 232 MET cc_start: 0.5995 (mpt) cc_final: 0.5725 (mmm) REVERT: C 360 ARG cc_start: 0.5708 (OUTLIER) cc_final: 0.4340 (mpp-170) REVERT: C 541 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: C 560 SER cc_start: 0.9198 (OUTLIER) cc_final: 0.8864 (t) REVERT: C 607 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6943 (mm-30) REVERT: C 846 MET cc_start: 0.4451 (tpp) cc_final: 0.4131 (ptt) outliers start: 81 outliers final: 45 residues processed: 221 average time/residue: 0.6814 time to fit residues: 165.7668 Evaluate side-chains 203 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 142 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 810 TYR Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 856 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 810 TYR Chi-restraints excluded: chain C residue 835 PHE Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 849 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 115 optimal weight: 3.9990 chunk 8 optimal weight: 0.0870 chunk 26 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 161 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.8964 ------------------------------------------------------------------------------- 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 = 0.4317 r_free = 0.4317 target = 0.215760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141076 restraints weight = 13356.084| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.85 r_work: 0.3229 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17169 Z= 0.188 Angle : 0.646 9.205 23295 Z= 0.349 Chirality : 0.046 0.222 2553 Planarity : 0.005 0.041 3018 Dihedral : 7.860 63.757 2518 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.52 % Allowed : 17.75 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.18), residues: 2061 helix: 2.82 (0.19), residues: 693 sheet: 0.75 (0.22), residues: 534 loop : -0.28 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 562 TYR 0.016 0.002 TYR B 849 PHE 0.019 0.002 PHE B 287 TRP 0.015 0.002 TRP C 539 HIS 0.005 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00395 (17151) covalent geometry : angle 0.64131 (23253) SS BOND : bond 0.01407 ( 12) SS BOND : angle 1.82844 ( 24) hydrogen bonds : bond 0.05894 ( 836) hydrogen bonds : angle 4.81537 ( 2484) link_NAG-ASN : bond 0.00165 ( 6) link_NAG-ASN : angle 1.88371 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 150 time to evaluate : 0.627 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: A 187 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: A 232 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.5842 (mmm) REVERT: A 275 GLU cc_start: 0.7820 (tt0) cc_final: 0.6961 (mm-30) REVERT: A 360 ARG cc_start: 0.5794 (OUTLIER) cc_final: 0.5291 (mpp-170) REVERT: A 416 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7082 (m-30) REVERT: A 541 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8228 (mp0) REVERT: A 592 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7265 (ttp-170) REVERT: A 692 HIS cc_start: 0.7665 (m90) cc_final: 0.7242 (m-70) REVERT: A 850 MET cc_start: 0.5657 (tpt) cc_final: 0.5284 (tpt) REVERT: B 187 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6958 (pm20) REVERT: B 214 VAL cc_start: 0.6783 (OUTLIER) cc_final: 0.6513 (t) REVERT: B 360 ARG cc_start: 0.5930 (OUTLIER) cc_final: 0.4105 (mpp-170) REVERT: B 592 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7222 (ttp-170) REVERT: B 731 MET cc_start: 0.5721 (OUTLIER) cc_final: 0.5206 (ptp) REVERT: B 846 MET cc_start: 0.4001 (tpp) cc_final: 0.3402 (mtm) REVERT: C 167 ASP cc_start: 0.7688 (p0) cc_final: 0.7204 (m-30) REVERT: C 187 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6911 (pm20) REVERT: C 204 LYS cc_start: 0.4665 (OUTLIER) cc_final: 0.4145 (pmtt) REVERT: C 360 ARG cc_start: 0.5684 (OUTLIER) cc_final: 0.4551 (mpp-170) REVERT: C 541 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: C 846 MET cc_start: 0.4549 (tpp) cc_final: 0.4210 (ptt) outliers start: 97 outliers final: 50 residues processed: 232 average time/residue: 0.6027 time to fit residues: 155.1706 Evaluate side-chains 207 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 142 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 810 TYR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 810 TYR Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 849 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 197 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.215174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139423 restraints weight = 13240.770| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.90 r_work: 0.3228 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 17169 Z= 0.215 Angle : 0.689 7.318 23295 Z= 0.371 Chirality : 0.047 0.224 2553 Planarity : 0.005 0.042 3018 Dihedral : 8.059 64.565 2515 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.63 % Allowed : 17.63 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.18), residues: 2061 helix: 2.72 (0.19), residues: 693 sheet: 0.71 (0.22), residues: 534 loop : -0.32 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 562 TYR 0.015 0.002 TYR C 702 PHE 0.020 0.002 PHE B 287 TRP 0.016 0.002 TRP C 539 HIS 0.006 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00461 (17151) covalent geometry : angle 0.68261 (23253) SS BOND : bond 0.01636 ( 12) SS BOND : angle 2.46281 ( 24) hydrogen bonds : bond 0.06082 ( 836) hydrogen bonds : angle 4.82786 ( 2484) link_NAG-ASN : bond 0.00198 ( 6) link_NAG-ASN : angle 1.99738 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 148 time to evaluate : 0.631 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: A 187 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: A 232 MET cc_start: 0.6232 (OUTLIER) cc_final: 0.5852 (mmm) REVERT: A 275 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6988 (mm-30) REVERT: A 323 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6131 (m-30) REVERT: A 360 ARG cc_start: 0.5831 (OUTLIER) cc_final: 0.5239 (mpp-170) REVERT: A 416 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7047 (m-30) REVERT: A 541 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8234 (mp0) REVERT: A 592 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7136 (ttp-170) REVERT: A 607 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6909 (mm-30) REVERT: A 692 HIS cc_start: 0.7677 (m90) cc_final: 0.7215 (m-70) REVERT: A 850 MET cc_start: 0.5626 (tpt) cc_final: 0.5376 (tpt) REVERT: B 187 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6948 (pm20) REVERT: B 360 ARG cc_start: 0.5977 (OUTLIER) cc_final: 0.4126 (mpp-170) REVERT: B 506 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6670 (mt) REVERT: B 592 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7267 (ttp-170) REVERT: B 607 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6897 (mm-30) REVERT: B 731 MET cc_start: 0.5757 (OUTLIER) cc_final: 0.5268 (ptp) REVERT: B 846 MET cc_start: 0.4089 (tpp) cc_final: 0.3325 (mtt) REVERT: C 187 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6964 (pm20) REVERT: C 204 LYS cc_start: 0.4664 (OUTLIER) cc_final: 0.4068 (pmtt) REVERT: C 360 ARG cc_start: 0.5700 (OUTLIER) cc_final: 0.4718 (mpp-170) REVERT: C 541 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: C 806 MET cc_start: 0.4555 (mmt) cc_final: 0.4051 (mmm) REVERT: C 846 MET cc_start: 0.4436 (tpp) cc_final: 0.4054 (ptt) outliers start: 99 outliers final: 59 residues processed: 233 average time/residue: 0.5758 time to fit residues: 149.5303 Evaluate side-chains 218 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 142 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 810 TYR Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 810 TYR Chi-restraints excluded: chain C residue 840 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 205 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.215913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133957 restraints weight = 13160.729| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.95 r_work: 0.3181 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17169 Z= 0.176 Angle : 0.631 8.942 23295 Z= 0.340 Chirality : 0.045 0.206 2553 Planarity : 0.005 0.041 3018 Dihedral : 7.838 62.779 2515 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.18 % Allowed : 17.86 % Favored : 76.96 % 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: 1.58 (0.18), residues: 2061 helix: 2.87 (0.19), residues: 690 sheet: 0.74 (0.22), residues: 534 loop : -0.30 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 328 TYR 0.013 0.002 TYR B 282 PHE 0.018 0.002 PHE B 287 TRP 0.014 0.002 TRP C 539 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00369 (17151) covalent geometry : angle 0.62659 (23253) SS BOND : bond 0.01376 ( 12) SS BOND : angle 1.76705 ( 24) hydrogen bonds : bond 0.05585 ( 836) hydrogen bonds : angle 4.68862 ( 2484) link_NAG-ASN : bond 0.00107 ( 6) link_NAG-ASN : angle 1.79655 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 146 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7135 (pm20) REVERT: A 212 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7117 (mppt) REVERT: A 214 VAL cc_start: 0.6876 (OUTLIER) cc_final: 0.6569 (t) REVERT: A 275 GLU cc_start: 0.7952 (tt0) cc_final: 0.7109 (mm-30) REVERT: A 323 ASP cc_start: 0.6595 (OUTLIER) cc_final: 0.6185 (m-30) REVERT: A 360 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5366 (mpp-170) REVERT: A 416 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7141 (m-30) REVERT: A 541 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: A 592 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7271 (ttp-170) REVERT: A 607 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6847 (mm-30) REVERT: A 622 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8081 (tp30) REVERT: A 692 HIS cc_start: 0.7726 (m90) cc_final: 0.7264 (m-70) REVERT: B 187 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7022 (pm20) REVERT: B 212 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7116 (mptp) REVERT: B 214 VAL cc_start: 0.6687 (OUTLIER) cc_final: 0.6418 (t) REVERT: B 242 ARG cc_start: 0.4345 (OUTLIER) cc_final: 0.4024 (mmp-170) REVERT: B 275 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: B 360 ARG cc_start: 0.5941 (OUTLIER) cc_final: 0.4044 (mpp-170) REVERT: B 506 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6532 (mt) REVERT: B 592 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7469 (ttp-170) REVERT: B 607 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6857 (mm-30) REVERT: B 731 MET cc_start: 0.5790 (OUTLIER) cc_final: 0.5294 (ptp) REVERT: B 846 MET cc_start: 0.4178 (tpp) cc_final: 0.3419 (mtt) REVERT: C 167 ASP cc_start: 0.7695 (p0) cc_final: 0.7271 (m-30) REVERT: C 187 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: C 204 LYS cc_start: 0.4651 (OUTLIER) cc_final: 0.4096 (pmtt) REVERT: C 360 ARG cc_start: 0.5698 (OUTLIER) cc_final: 0.4905 (mpp-170) REVERT: C 541 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8449 (mm-30) REVERT: C 560 SER cc_start: 0.9197 (OUTLIER) cc_final: 0.8851 (t) REVERT: C 806 MET cc_start: 0.4503 (mmt) cc_final: 0.4010 (mmm) REVERT: C 846 MET cc_start: 0.4528 (tpp) cc_final: 0.4133 (ptt) outliers start: 91 outliers final: 48 residues processed: 223 average time/residue: 0.6265 time to fit residues: 155.0222 Evaluate side-chains 216 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 145 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 810 TYR Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 810 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.0670 chunk 194 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.216645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.138190 restraints weight = 13159.361| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.88 r_work: 0.3189 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17169 Z= 0.154 Angle : 0.609 9.346 23295 Z= 0.327 Chirality : 0.044 0.196 2553 Planarity : 0.004 0.041 3018 Dihedral : 7.535 61.954 2511 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.18 % Allowed : 18.15 % Favored : 76.68 % 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: 1.69 (0.18), residues: 2061 helix: 2.98 (0.19), residues: 690 sheet: 0.80 (0.23), residues: 534 loop : -0.24 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.011 0.002 TYR B 282 PHE 0.017 0.002 PHE B 287 TRP 0.012 0.002 TRP C 539 HIS 0.002 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00319 (17151) covalent geometry : angle 0.60494 (23253) SS BOND : bond 0.01196 ( 12) SS BOND : angle 1.76029 ( 24) hydrogen bonds : bond 0.05252 ( 836) hydrogen bonds : angle 4.59257 ( 2484) link_NAG-ASN : bond 0.00104 ( 6) link_NAG-ASN : angle 1.69999 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 151 time to evaluate : 0.728 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: A 187 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7146 (pm20) REVERT: A 212 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7127 (mppt) REVERT: A 214 VAL cc_start: 0.6811 (OUTLIER) cc_final: 0.6539 (t) REVERT: A 275 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7087 (mm-30) REVERT: A 360 ARG cc_start: 0.5805 (OUTLIER) cc_final: 0.5339 (mpp-170) REVERT: A 432 THR cc_start: 0.7047 (p) cc_final: 0.6741 (t) REVERT: A 541 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: A 592 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7231 (ttp-170) REVERT: A 607 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6854 (mm-30) REVERT: A 692 HIS cc_start: 0.7742 (m90) cc_final: 0.7285 (m-70) REVERT: B 187 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7021 (pm20) REVERT: B 212 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7113 (mptp) REVERT: B 214 VAL cc_start: 0.6652 (OUTLIER) cc_final: 0.6424 (t) REVERT: B 275 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7205 (mm-30) REVERT: B 360 ARG cc_start: 0.5941 (OUTLIER) cc_final: 0.4071 (mpp-170) REVERT: B 506 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6506 (mt) REVERT: B 592 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7458 (mtp180) REVERT: B 607 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6928 (mm-30) REVERT: B 731 MET cc_start: 0.5749 (OUTLIER) cc_final: 0.5252 (ptp) REVERT: B 846 MET cc_start: 0.4243 (tpp) cc_final: 0.3470 (mtt) REVERT: C 167 ASP cc_start: 0.7672 (p0) cc_final: 0.7391 (m-30) REVERT: C 187 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7003 (pm20) REVERT: C 204 LYS cc_start: 0.4531 (OUTLIER) cc_final: 0.3986 (pmtt) REVERT: C 242 ARG cc_start: 0.4944 (OUTLIER) cc_final: 0.4383 (mmt180) REVERT: C 360 ARG cc_start: 0.5687 (OUTLIER) cc_final: 0.5217 (mpp-170) REVERT: C 560 SER cc_start: 0.9191 (OUTLIER) cc_final: 0.8870 (t) REVERT: C 806 MET cc_start: 0.4306 (mmt) cc_final: 0.3863 (mmm) REVERT: C 846 MET cc_start: 0.4553 (tpp) cc_final: 0.4176 (ptt) outliers start: 91 outliers final: 55 residues processed: 225 average time/residue: 0.5741 time to fit residues: 144.0634 Evaluate side-chains 225 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 150 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 810 TYR Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 810 TYR Chi-restraints excluded: chain C residue 847 ILE Chi-restraints excluded: chain C residue 849 TYR Chi-restraints excluded: chain C residue 850 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 89 optimal weight: 0.0470 chunk 47 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 163 optimal weight: 0.3980 chunk 192 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.217739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.138093 restraints weight = 13175.363| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.91 r_work: 0.3220 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17169 Z= 0.126 Angle : 0.562 8.934 23295 Z= 0.302 Chirality : 0.042 0.181 2553 Planarity : 0.004 0.040 3018 Dihedral : 6.933 59.282 2505 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.15 % Allowed : 19.28 % Favored : 76.56 % 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: 1.83 (0.18), residues: 2061 helix: 3.13 (0.19), residues: 690 sheet: 0.86 (0.23), residues: 534 loop : -0.18 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.023 0.001 TYR C 284 PHE 0.016 0.001 PHE B 534 TRP 0.015 0.002 TRP C 247 HIS 0.002 0.000 HIS A 657 Details of bonding type rmsd covalent geometry : bond 0.00252 (17151) covalent geometry : angle 0.55791 (23253) SS BOND : bond 0.00997 ( 12) SS BOND : angle 1.62163 ( 24) hydrogen bonds : bond 0.04810 ( 836) hydrogen bonds : angle 4.43880 ( 2484) link_NAG-ASN : bond 0.00151 ( 6) link_NAG-ASN : angle 1.56858 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 159 time to evaluate : 0.657 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: A 187 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7105 (pm20) REVERT: A 212 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7107 (mppt) REVERT: A 214 VAL cc_start: 0.6774 (OUTLIER) cc_final: 0.6563 (t) REVERT: A 275 GLU cc_start: 0.7870 (tt0) cc_final: 0.7030 (mm-30) REVERT: A 432 THR cc_start: 0.7053 (p) cc_final: 0.6753 (t) REVERT: A 541 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: A 560 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8830 (t) REVERT: A 607 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6826 (mm-30) REVERT: A 692 HIS cc_start: 0.7742 (m90) cc_final: 0.7314 (m-70) REVERT: B 167 ASP cc_start: 0.7613 (p0) cc_final: 0.7382 (p0) REVERT: B 187 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: B 212 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7121 (mptp) REVERT: B 360 ARG cc_start: 0.5838 (OUTLIER) cc_final: 0.4051 (mpp-170) REVERT: B 416 ASP cc_start: 0.7510 (m-30) cc_final: 0.6963 (t0) REVERT: B 506 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6442 (mt) REVERT: B 607 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6877 (mm-30) REVERT: B 731 MET cc_start: 0.5748 (OUTLIER) cc_final: 0.5257 (ptp) REVERT: B 846 MET cc_start: 0.4157 (tpp) cc_final: 0.3411 (mtt) REVERT: C 187 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: C 204 LYS cc_start: 0.4529 (OUTLIER) cc_final: 0.4011 (pmtt) REVERT: C 242 ARG cc_start: 0.4912 (OUTLIER) cc_final: 0.4354 (mmt180) REVERT: C 531 LEU cc_start: 0.8823 (tp) cc_final: 0.8619 (tm) REVERT: C 560 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8862 (t) REVERT: C 661 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6742 (ptm160) REVERT: C 806 MET cc_start: 0.4417 (mmt) cc_final: 0.3941 (mmm) REVERT: C 846 MET cc_start: 0.4569 (tpp) cc_final: 0.3739 (mtm) outliers start: 73 outliers final: 35 residues processed: 220 average time/residue: 0.6156 time to fit residues: 150.5090 Evaluate side-chains 202 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 810 TYR Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 810 TYR Chi-restraints excluded: chain C residue 850 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 158 optimal weight: 8.9990 chunk 198 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 66 optimal weight: 0.0270 chunk 151 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.216733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.144685 restraints weight = 13283.399| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.24 r_work: 0.3189 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17169 Z= 0.152 Angle : 0.603 10.720 23295 Z= 0.322 Chirality : 0.043 0.189 2553 Planarity : 0.004 0.040 3018 Dihedral : 6.887 61.505 2501 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.92 % Allowed : 19.23 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.18), residues: 2061 helix: 3.12 (0.18), residues: 690 sheet: 0.88 (0.23), residues: 534 loop : -0.18 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 592 TYR 0.019 0.002 TYR C 284 PHE 0.017 0.002 PHE B 287 TRP 0.016 0.002 TRP C 247 HIS 0.003 0.001 HIS B 657 Details of bonding type rmsd covalent geometry : bond 0.00313 (17151) covalent geometry : angle 0.59935 (23253) SS BOND : bond 0.01166 ( 12) SS BOND : angle 1.72919 ( 24) hydrogen bonds : bond 0.05184 ( 836) hydrogen bonds : angle 4.49711 ( 2484) link_NAG-ASN : bond 0.00115 ( 6) link_NAG-ASN : angle 1.65029 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 149 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7162 (pm20) REVERT: A 212 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7148 (mppt) REVERT: A 214 VAL cc_start: 0.6775 (OUTLIER) cc_final: 0.6561 (t) REVERT: A 275 GLU cc_start: 0.7935 (tt0) cc_final: 0.7102 (mm-30) REVERT: A 416 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7220 (m-30) REVERT: A 432 THR cc_start: 0.7110 (p) cc_final: 0.6796 (t) REVERT: A 541 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: A 607 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6885 (mm-30) REVERT: A 692 HIS cc_start: 0.7790 (m90) cc_final: 0.7360 (m-70) REVERT: B 187 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7071 (pm20) REVERT: B 212 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7166 (mptp) REVERT: B 360 ARG cc_start: 0.5893 (OUTLIER) cc_final: 0.4033 (mpp-170) REVERT: B 406 ARG cc_start: 0.5741 (OUTLIER) cc_final: 0.4743 (mtt180) REVERT: B 506 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6437 (mt) REVERT: B 607 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6897 (mm-30) REVERT: B 731 MET cc_start: 0.5770 (OUTLIER) cc_final: 0.5253 (ptp) REVERT: B 846 MET cc_start: 0.4151 (tpp) cc_final: 0.3354 (mtt) REVERT: C 187 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7040 (pm20) REVERT: C 204 LYS cc_start: 0.4563 (OUTLIER) cc_final: 0.3969 (pmtt) REVERT: C 242 ARG cc_start: 0.4883 (OUTLIER) cc_final: 0.4335 (mmt180) REVERT: C 360 ARG cc_start: 0.5665 (OUTLIER) cc_final: 0.5388 (mpp-170) REVERT: C 560 SER cc_start: 0.9198 (OUTLIER) cc_final: 0.8882 (t) REVERT: C 806 MET cc_start: 0.4338 (mmt) cc_final: 0.3888 (mmm) REVERT: C 846 MET cc_start: 0.4570 (tpp) cc_final: 0.3727 (mtm) outliers start: 69 outliers final: 43 residues processed: 207 average time/residue: 0.6393 time to fit residues: 146.7825 Evaluate side-chains 208 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 149 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 810 TYR Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 810 TYR Chi-restraints excluded: chain C residue 850 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 180 optimal weight: 3.9990 chunk 201 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4327 r_free = 0.4327 target = 0.216752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.145188 restraints weight = 13229.029| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.96 r_work: 0.3176 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17169 Z= 0.149 Angle : 0.598 9.812 23295 Z= 0.321 Chirality : 0.043 0.188 2553 Planarity : 0.004 0.040 3018 Dihedral : 6.801 60.697 2501 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.81 % Allowed : 19.40 % Favored : 76.79 % 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 (0.18), residues: 2061 helix: 3.08 (0.19), residues: 693 sheet: 0.89 (0.23), residues: 534 loop : -0.14 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 592 TYR 0.018 0.002 TYR C 284 PHE 0.016 0.002 PHE B 287 TRP 0.020 0.002 TRP C 247 HIS 0.003 0.001 HIS B 657 Details of bonding type rmsd covalent geometry : bond 0.00308 (17151) covalent geometry : angle 0.59287 (23253) SS BOND : bond 0.01160 ( 12) SS BOND : angle 2.13564 ( 24) hydrogen bonds : bond 0.05162 ( 836) hydrogen bonds : angle 4.47379 ( 2484) link_NAG-ASN : bond 0.00127 ( 6) link_NAG-ASN : angle 1.60227 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 150 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: A 212 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7138 (mppt) REVERT: A 214 VAL cc_start: 0.6739 (OUTLIER) cc_final: 0.6528 (t) REVERT: A 275 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7149 (mm-30) REVERT: A 360 ARG cc_start: 0.5862 (OUTLIER) cc_final: 0.5346 (mpp-170) REVERT: A 416 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: A 432 THR cc_start: 0.7145 (p) cc_final: 0.6839 (t) REVERT: A 541 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8341 (mp0) REVERT: A 607 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6922 (mm-30) REVERT: A 692 HIS cc_start: 0.7797 (m90) cc_final: 0.7353 (m-70) REVERT: B 187 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7076 (pm20) REVERT: B 212 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7159 (mptp) REVERT: B 323 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6181 (m-30) REVERT: B 360 ARG cc_start: 0.5935 (OUTLIER) cc_final: 0.4048 (mpp-170) REVERT: B 406 ARG cc_start: 0.5753 (OUTLIER) cc_final: 0.4743 (mtt180) REVERT: B 416 ASP cc_start: 0.7590 (m-30) cc_final: 0.7051 (t0) REVERT: B 506 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6372 (mt) REVERT: B 607 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6919 (mm-30) REVERT: B 731 MET cc_start: 0.5739 (OUTLIER) cc_final: 0.5228 (ptp) REVERT: B 846 MET cc_start: 0.4180 (tpp) cc_final: 0.3553 (mtm) REVERT: C 187 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7038 (pm20) REVERT: C 204 LYS cc_start: 0.4504 (OUTLIER) cc_final: 0.3902 (pmtt) REVERT: C 242 ARG cc_start: 0.4865 (OUTLIER) cc_final: 0.4305 (mmt180) REVERT: C 560 SER cc_start: 0.9206 (OUTLIER) cc_final: 0.8889 (t) REVERT: C 806 MET cc_start: 0.4432 (mmt) cc_final: 0.3983 (mmm) REVERT: C 846 MET cc_start: 0.4678 (tpp) cc_final: 0.4242 (ptp) outliers start: 67 outliers final: 42 residues processed: 204 average time/residue: 0.6129 time to fit residues: 139.2396 Evaluate side-chains 210 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 150 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 810 TYR Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 728 ASN Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 810 TYR Chi-restraints excluded: chain C residue 850 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 202 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 53 optimal weight: 0.0980 chunk 206 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.4342 r_free = 0.4342 target = 0.218403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.138124 restraints weight = 13227.107| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.98 r_work: 0.3239 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17169 Z= 0.116 Angle : 0.548 11.969 23295 Z= 0.292 Chirality : 0.041 0.168 2553 Planarity : 0.004 0.039 3018 Dihedral : 6.317 59.510 2501 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.84 % Allowed : 20.19 % Favored : 76.96 % 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 (0.19), residues: 2061 helix: 3.23 (0.19), residues: 693 sheet: 0.95 (0.23), residues: 534 loop : -0.09 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.017 0.001 TYR C 284 PHE 0.017 0.001 PHE B 534 TRP 0.022 0.002 TRP C 247 HIS 0.002 0.000 HIS A 657 Details of bonding type rmsd covalent geometry : bond 0.00231 (17151) covalent geometry : angle 0.54379 (23253) SS BOND : bond 0.00863 ( 12) SS BOND : angle 1.86869 ( 24) hydrogen bonds : bond 0.04524 ( 836) hydrogen bonds : angle 4.27961 ( 2484) link_NAG-ASN : bond 0.00215 ( 6) link_NAG-ASN : angle 1.43089 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: A 212 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7113 (mppt) REVERT: A 275 GLU cc_start: 0.7882 (tt0) cc_final: 0.7039 (mm-30) REVERT: A 432 THR cc_start: 0.7075 (p) cc_final: 0.6788 (t) REVERT: A 541 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8270 (mp0) REVERT: A 560 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8853 (t) REVERT: A 607 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6794 (mm-30) REVERT: A 661 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7040 (ptm160) REVERT: A 692 HIS cc_start: 0.7739 (m90) cc_final: 0.7323 (m-70) REVERT: B 167 ASP cc_start: 0.7533 (p0) cc_final: 0.6967 (m-30) REVERT: B 212 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7167 (mptp) REVERT: B 360 ARG cc_start: 0.5817 (OUTLIER) cc_final: 0.3987 (mpp-170) REVERT: B 416 ASP cc_start: 0.7390 (m-30) cc_final: 0.6808 (t0) REVERT: B 506 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6135 (mt) REVERT: B 607 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6832 (mm-30) REVERT: B 731 MET cc_start: 0.5722 (OUTLIER) cc_final: 0.5224 (ptp) REVERT: B 846 MET cc_start: 0.4125 (tpp) cc_final: 0.3548 (mtm) REVERT: C 204 LYS cc_start: 0.4456 (OUTLIER) cc_final: 0.3923 (pmtt) REVERT: C 232 MET cc_start: 0.6072 (mpt) cc_final: 0.5816 (mmm) REVERT: C 242 ARG cc_start: 0.4735 (OUTLIER) cc_final: 0.4170 (mmt180) REVERT: C 416 ASP cc_start: 0.7394 (m-30) cc_final: 0.6831 (t0) REVERT: C 560 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8859 (t) REVERT: C 661 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7222 (ptm160) REVERT: C 806 MET cc_start: 0.4359 (mmt) cc_final: 0.3935 (mmm) REVERT: C 846 MET cc_start: 0.4546 (tpp) cc_final: 0.4128 (ptp) outliers start: 50 outliers final: 29 residues processed: 194 average time/residue: 0.6131 time to fit residues: 132.0869 Evaluate side-chains 190 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 810 TYR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 661 ARG Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 810 TYR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 782 LEU Chi-restraints excluded: chain C residue 810 TYR Chi-restraints excluded: chain C residue 850 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 28 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 151 optimal weight: 0.0020 chunk 201 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 = 0.4337 r_free = 0.4337 target = 0.217889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.139829 restraints weight = 13200.650| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.96 r_work: 0.3211 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17169 Z= 0.123 Angle : 0.556 10.629 23295 Z= 0.297 Chirality : 0.042 0.171 2553 Planarity : 0.004 0.039 3018 Dihedral : 6.312 59.247 2499 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.90 % Allowed : 20.02 % Favored : 77.08 % 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 (0.19), residues: 2061 helix: 3.23 (0.18), residues: 693 sheet: 0.95 (0.23), residues: 534 loop : -0.09 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.015 0.001 TYR C 284 PHE 0.015 0.001 PHE B 534 TRP 0.017 0.002 TRP C 247 HIS 0.002 0.000 HIS C 657 Details of bonding type rmsd covalent geometry : bond 0.00248 (17151) covalent geometry : angle 0.55127 (23253) SS BOND : bond 0.00930 ( 12) SS BOND : angle 1.84306 ( 24) hydrogen bonds : bond 0.04717 ( 836) hydrogen bonds : angle 4.30960 ( 2484) link_NAG-ASN : bond 0.00181 ( 6) link_NAG-ASN : angle 1.50006 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10248.48 seconds wall clock time: 173 minutes 47.18 seconds (10427.18 seconds total)