Starting phenix.real_space_refine on Sat Aug 23 17:46:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jrn_36599/08_2025/8jrn_36599.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jrn_36599/08_2025/8jrn_36599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jrn_36599/08_2025/8jrn_36599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jrn_36599/08_2025/8jrn_36599.map" model { file = "/net/cci-nas-00/data/ceres_data/8jrn_36599/08_2025/8jrn_36599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jrn_36599/08_2025/8jrn_36599.cif" } resolution = 2.6 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 92 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 78 5.16 5 C 8720 2.51 5 N 2294 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13672 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1191 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "C" Number of atoms: 5643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5643 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 28, 'TRANS': 660} Chain breaks: 1 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1191 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "A" Number of atoms: 5643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5643 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 28, 'TRANS': 660} Chain breaks: 1 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 241 SG CYS D 37 80.325 76.845 88.839 1.00 26.36 S ATOM 266 SG CYS D 40 81.531 74.319 91.219 1.00 38.33 S ATOM 522 SG CYS D 70 82.722 74.229 87.529 1.00 39.32 S ATOM 545 SG CYS D 73 79.254 73.116 88.390 1.00 44.29 S ATOM 864 SG CYS D 110 81.003 74.553 71.069 1.00 32.36 S ATOM 886 SG CYS D 113 83.147 75.923 73.849 1.00 28.84 S ATOM 1148 SG CYS D 143 84.650 74.990 70.447 1.00 41.28 S ATOM 1168 SG CYS D 146 83.506 72.219 72.728 1.00 41.86 S ATOM 7075 SG CYS B 37 63.189 34.539 88.839 1.00 26.36 S ATOM 7100 SG CYS B 40 61.983 37.065 91.219 1.00 38.33 S ATOM 7356 SG CYS B 70 60.792 37.155 87.529 1.00 39.32 S ATOM 7379 SG CYS B 73 64.260 38.268 88.390 1.00 44.29 S ATOM 7698 SG CYS B 110 62.511 36.831 71.069 1.00 32.36 S ATOM 7720 SG CYS B 113 60.367 35.461 73.849 1.00 28.84 S ATOM 7982 SG CYS B 143 58.864 36.394 70.447 1.00 41.28 S ATOM 8002 SG CYS B 146 60.008 39.165 72.728 1.00 41.86 S Time building chain proxies: 2.66, per 1000 atoms: 0.19 Number of scatterers: 13672 At special positions: 0 Unit cell: (144.585, 112.455, 109.242, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 78 16.00 O 2576 8.00 N 2294 7.00 C 8720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 460.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 70 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 73 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 110 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 143 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 113 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 146 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 70 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 40 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 37 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 73 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 110 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 143 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 146 " Number of angles added : 24 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 14 sheets defined 61.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'D' and resid 18 through 26 Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 70 through 85 Processing helix chain 'D' and resid 91 through 100 Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 118 through 128 Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'C' and resid 131 through 140 Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'C' and resid 159 through 165 removed outlier: 3.502A pdb=" N GLN C 165 " --> pdb=" O GLU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 247 removed outlier: 3.615A pdb=" N ILE C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 273 removed outlier: 3.582A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Proline residue: C 265 - end of helix removed outlier: 3.635A pdb=" N CYS C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP C 270 " --> pdb=" O ASN C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 removed outlier: 4.086A pdb=" N ARG C 279 " --> pdb=" O ASN C 275 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 275 through 280' Processing helix chain 'C' and resid 281 through 283 No H-bonds generated for 'chain 'C' and resid 281 through 283' Processing helix chain 'C' and resid 284 through 292 removed outlier: 3.588A pdb=" N ILE C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 298 Processing helix chain 'C' and resid 304 through 314 removed outlier: 3.544A pdb=" N LEU C 308 " --> pdb=" O MET C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 330 removed outlier: 3.872A pdb=" N LYS C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 354 removed outlier: 3.599A pdb=" N PHE C 343 " --> pdb=" O MET C 339 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.612A pdb=" N MET C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 413 Processing helix chain 'C' and resid 426 through 433 removed outlier: 3.601A pdb=" N THR C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.583A pdb=" N ILE C 450 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 456 Processing helix chain 'C' and resid 459 through 469 removed outlier: 3.606A pdb=" N THR C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 Proline residue: C 481 - end of helix Processing helix chain 'C' and resid 485 through 515 Processing helix chain 'C' and resid 528 through 530 No H-bonds generated for 'chain 'C' and resid 528 through 530' Processing helix chain 'C' and resid 531 through 547 Processing helix chain 'C' and resid 548 through 553 Processing helix chain 'C' and resid 568 through 583 Processing helix chain 'C' and resid 584 through 588 Processing helix chain 'C' and resid 608 through 625 Processing helix chain 'C' and resid 634 through 642 removed outlier: 3.914A pdb=" N TYR C 638 " --> pdb=" O PRO C 634 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 650 through 655 removed outlier: 3.543A pdb=" N SER C 654 " --> pdb=" O ASP C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 667 removed outlier: 3.961A pdb=" N LEU C 665 " --> pdb=" O SER C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 676 Processing helix chain 'C' and resid 709 through 723 Processing helix chain 'C' and resid 726 through 742 removed outlier: 3.977A pdb=" N VAL C 740 " --> pdb=" O GLY C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 750 Processing helix chain 'C' and resid 751 through 760 removed outlier: 3.874A pdb=" N GLU C 756 " --> pdb=" O PRO C 752 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU C 757 " --> pdb=" O GLU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 774 Processing helix chain 'C' and resid 784 through 796 Processing helix chain 'C' and resid 798 through 811 Processing helix chain 'C' and resid 842 through 844 No H-bonds generated for 'chain 'C' and resid 842 through 844' Processing helix chain 'C' and resid 854 through 867 Processing helix chain 'B' and resid 18 through 26 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 70 through 85 Processing helix chain 'B' and resid 91 through 100 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.502A pdb=" N GLN A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 removed outlier: 3.615A pdb=" N ILE A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 273 removed outlier: 3.582A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Proline residue: A 265 - end of helix removed outlier: 3.635A pdb=" N CYS A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 4.086A pdb=" N ARG A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 280' Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.588A pdb=" N ILE A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 304 through 314 removed outlier: 3.544A pdb=" N LEU A 308 " --> pdb=" O MET A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 330 removed outlier: 3.872A pdb=" N LYS A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 354 removed outlier: 3.599A pdb=" N PHE A 343 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.612A pdb=" N MET A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'A' and resid 426 through 433 removed outlier: 3.601A pdb=" N THR A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.583A pdb=" N ILE A 450 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 Processing helix chain 'A' and resid 459 through 469 removed outlier: 3.606A pdb=" N THR A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 485 through 515 Processing helix chain 'A' and resid 528 through 530 No H-bonds generated for 'chain 'A' and resid 528 through 530' Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 568 through 583 Processing helix chain 'A' and resid 584 through 588 Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 634 through 642 removed outlier: 3.914A pdb=" N TYR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 650 through 655 removed outlier: 3.543A pdb=" N SER A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 667 removed outlier: 3.961A pdb=" N LEU A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 709 through 723 Processing helix chain 'A' and resid 726 through 742 removed outlier: 3.977A pdb=" N VAL A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 Processing helix chain 'A' and resid 751 through 760 removed outlier: 3.874A pdb=" N GLU A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 774 Processing helix chain 'A' and resid 784 through 796 Processing helix chain 'A' and resid 798 through 811 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 854 through 867 Processing sheet with id=AA1, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'D' and resid 86 through 90 removed outlier: 6.738A pdb=" N ASN D 134 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER D 89 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE D 132 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARG D 109 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 387 through 388 removed outlier: 6.595A pdb=" N GLU C 387 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 522 through 527 Processing sheet with id=AA5, first strand: chain 'C' and resid 590 through 593 Processing sheet with id=AA6, first strand: chain 'C' and resid 681 through 685 Processing sheet with id=AA7, first strand: chain 'C' and resid 775 through 777 removed outlier: 6.490A pdb=" N GLU C 775 " --> pdb=" O ILE C 827 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS C 829 " --> pdb=" O GLU C 775 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP C 777 " --> pdb=" O LYS C 829 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE C 826 " --> pdb=" O LEU C 847 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU C 849 " --> pdb=" O ILE C 826 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA C 828 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA9, first strand: chain 'B' and resid 86 through 90 removed outlier: 6.738A pdb=" N ASN B 134 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER B 89 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE B 132 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARG B 109 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.595A pdb=" N GLU A 387 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 522 through 527 Processing sheet with id=AB3, first strand: chain 'A' and resid 590 through 593 Processing sheet with id=AB4, first strand: chain 'A' and resid 681 through 685 Processing sheet with id=AB5, first strand: chain 'A' and resid 775 through 777 removed outlier: 6.490A pdb=" N GLU A 775 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS A 829 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP A 777 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE A 826 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU A 849 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA A 828 " --> pdb=" O LEU A 849 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1848 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.26 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: 4488 1.34 - 1.46: 3003 1.46 - 1.58: 6337 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 13948 Sorted by residual: bond pdb=" N LEU A 806 " pdb=" CA LEU A 806 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.34e+00 bond pdb=" N ASP A 397 " pdb=" CA ASP A 397 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.29e+00 bond pdb=" N ASP C 397 " pdb=" CA ASP C 397 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.23e-02 6.61e+03 5.78e+00 bond pdb=" N LEU C 806 " pdb=" CA LEU C 806 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.76e+00 bond pdb=" N THR C 809 " pdb=" CA THR C 809 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.28e-02 6.10e+03 5.55e+00 ... (remaining 13943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 18306 1.26 - 2.52: 402 2.52 - 3.79: 104 3.79 - 5.05: 18 5.05 - 6.31: 2 Bond angle restraints: 18832 Sorted by residual: angle pdb=" CA ASP A 396 " pdb=" C ASP A 396 " pdb=" O ASP A 396 " ideal model delta sigma weight residual 120.96 118.02 2.94 1.09e+00 8.42e-01 7.27e+00 angle pdb=" CA ASP C 396 " pdb=" C ASP C 396 " pdb=" O ASP C 396 " ideal model delta sigma weight residual 120.96 118.07 2.89 1.09e+00 8.42e-01 7.01e+00 angle pdb=" CA ASP C 397 " pdb=" C ASP C 397 " pdb=" O ASP C 397 " ideal model delta sigma weight residual 121.19 118.34 2.85 1.10e+00 8.26e-01 6.70e+00 angle pdb=" CA ASP A 397 " pdb=" C ASP A 397 " pdb=" O ASP A 397 " ideal model delta sigma weight residual 121.19 118.36 2.83 1.10e+00 8.26e-01 6.60e+00 angle pdb=" N ARG A 498 " pdb=" CA ARG A 498 " pdb=" C ARG A 498 " ideal model delta sigma weight residual 111.07 108.33 2.74 1.07e+00 8.73e-01 6.54e+00 ... (remaining 18827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 7299 17.67 - 35.35: 883 35.35 - 53.02: 270 53.02 - 70.70: 56 70.70 - 88.37: 20 Dihedral angle restraints: 8528 sinusoidal: 3612 harmonic: 4916 Sorted by residual: dihedral pdb=" CA ASP C 686 " pdb=" CB ASP C 686 " pdb=" CG ASP C 686 " pdb=" OD1 ASP C 686 " ideal model delta sinusoidal sigma weight residual -30.00 -89.60 59.60 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP A 686 " pdb=" CB ASP A 686 " pdb=" CG ASP A 686 " pdb=" OD1 ASP A 686 " ideal model delta sinusoidal sigma weight residual -30.00 -89.60 59.60 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CB GLU A 161 " pdb=" CG GLU A 161 " pdb=" CD GLU A 161 " pdb=" OE1 GLU A 161 " ideal model delta sinusoidal sigma weight residual 0.00 -88.34 88.34 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 8525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1334 0.032 - 0.064: 522 0.064 - 0.096: 143 0.096 - 0.128: 59 0.128 - 0.160: 2 Chirality restraints: 2060 Sorted by residual: chirality pdb=" CA GLN C 807 " pdb=" N GLN C 807 " pdb=" C GLN C 807 " pdb=" CB GLN C 807 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CA GLN A 807 " pdb=" N GLN A 807 " pdb=" C GLN A 807 " pdb=" CB GLN A 807 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE C 826 " pdb=" N ILE C 826 " pdb=" C ILE C 826 " pdb=" CB ILE C 826 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 2057 not shown) Planarity restraints: 2442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 444 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO A 445 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 444 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO C 445 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 445 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 445 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 764 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C ASN A 764 " -0.024 2.00e-02 2.50e+03 pdb=" O ASN A 764 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU A 765 " 0.008 2.00e-02 2.50e+03 ... (remaining 2439 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 38 2.45 - 3.06: 8875 3.06 - 3.68: 21456 3.68 - 4.29: 32921 4.29 - 4.90: 53217 Nonbonded interactions: 116507 Sorted by model distance: nonbonded pdb=" O GLU C 161 " pdb=" OE1 GLN C 165 " model vdw 1.840 3.040 nonbonded pdb=" O GLU A 161 " pdb=" OE1 GLN A 165 " model vdw 1.840 3.040 nonbonded pdb=" O ARG A 836 " pdb=" OH TYR A 852 " model vdw 2.158 3.040 nonbonded pdb=" O ARG C 836 " pdb=" OH TYR C 852 " model vdw 2.158 3.040 nonbonded pdb=" O LEU C 863 " pdb=" OG1 THR C 867 " model vdw 2.294 3.040 ... (remaining 116502 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: 0.01 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.090 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 0.047 13964 Z= 0.176 Angle : 0.519 6.311 18856 Z= 0.283 Chirality : 0.040 0.160 2060 Planarity : 0.003 0.041 2442 Dihedral : 17.312 88.369 5352 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.26 % Allowed : 25.33 % Favored : 74.41 % 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 aren not related in a simple way. whole: 0.37 (0.21), residues: 1648 helix: 0.20 (0.17), residues: 874 sheet: -1.41 (0.55), residues: 72 loop : 0.80 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 338 TYR 0.017 0.001 TYR D 77 PHE 0.012 0.001 PHE A 287 TRP 0.006 0.001 TRP B 139 HIS 0.003 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00376 (13948) covalent geometry : angle 0.50915 (18832) hydrogen bonds : bond 0.20972 ( 656) hydrogen bonds : angle 7.21062 ( 1848) metal coordination : bond 0.00331 ( 16) metal coordination : angle 2.82313 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 395 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: D 130 GLN cc_start: 0.8244 (mt0) cc_final: 0.7960 (mt0) REVERT: D 131 ARG cc_start: 0.8543 (mtm-85) cc_final: 0.8310 (mtt180) REVERT: C 132 LYS cc_start: 0.7390 (tppt) cc_final: 0.7176 (tppp) REVERT: C 264 SER cc_start: 0.7862 (m) cc_final: 0.7655 (m) REVERT: C 451 ASN cc_start: 0.8371 (t0) cc_final: 0.8148 (t0) REVERT: C 462 LYS cc_start: 0.8134 (ptpt) cc_final: 0.7894 (mtmm) REVERT: C 542 MET cc_start: 0.7160 (tpp) cc_final: 0.6955 (tpp) REVERT: C 586 ASP cc_start: 0.7550 (m-30) cc_final: 0.7234 (m-30) REVERT: C 593 ASP cc_start: 0.7032 (t0) cc_final: 0.6759 (t0) REVERT: C 692 MET cc_start: 0.6197 (mmm) cc_final: 0.5792 (mmm) REVERT: C 693 MET cc_start: 0.7108 (mtt) cc_final: 0.6471 (mtt) REVERT: C 768 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8186 (mm-40) REVERT: C 783 ASP cc_start: 0.7094 (m-30) cc_final: 0.6840 (m-30) REVERT: B 17 ARG cc_start: 0.6750 (ptm-80) cc_final: 0.6392 (ptm-80) REVERT: B 18 LYS cc_start: 0.8640 (mptp) cc_final: 0.8428 (mmtm) REVERT: B 130 GLN cc_start: 0.8115 (mt0) cc_final: 0.7770 (mt0) REVERT: B 131 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.8316 (mtt180) REVERT: A 132 LYS cc_start: 0.7372 (tppt) cc_final: 0.7141 (tptp) REVERT: A 338 ARG cc_start: 0.7379 (mtp85) cc_final: 0.7167 (mtp85) REVERT: A 355 GLU cc_start: 0.6572 (tm-30) cc_final: 0.6298 (tm-30) REVERT: A 447 GLU cc_start: 0.7086 (mp0) cc_final: 0.6876 (mp0) REVERT: A 460 MET cc_start: 0.8799 (mmm) cc_final: 0.8528 (mmt) REVERT: A 526 LYS cc_start: 0.7940 (tppp) cc_final: 0.7103 (ttmm) REVERT: A 542 MET cc_start: 0.7082 (tpp) cc_final: 0.6832 (tpp) REVERT: A 593 ASP cc_start: 0.7060 (t0) cc_final: 0.6753 (t0) REVERT: A 663 LYS cc_start: 0.7613 (ptmm) cc_final: 0.7350 (ttpp) REVERT: A 681 GLN cc_start: 0.7340 (tt0) cc_final: 0.6705 (tt0) REVERT: A 692 MET cc_start: 0.6081 (mmm) cc_final: 0.5663 (mmm) REVERT: A 693 MET cc_start: 0.6702 (mtt) cc_final: 0.6084 (mtt) REVERT: A 783 ASP cc_start: 0.7103 (m-30) cc_final: 0.6850 (m-30) outliers start: 4 outliers final: 2 residues processed: 397 average time/residue: 0.7746 time to fit residues: 331.1154 Evaluate side-chains 359 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 357 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain A residue 233 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 GLN D 43 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN C 321 GLN C 517 GLN C 520 ASN C 531 HIS C 584 ASN C 626 ASN C 715 ASN C 764 ASN C 795 HIS B 43 GLN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 531 HIS A 576 GLN A 602 ASN A 611 GLN A 626 ASN A 715 ASN A 764 ASN A 795 HIS A 807 GLN A 841 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122188 restraints weight = 18063.967| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.74 r_work: 0.3434 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13964 Z= 0.256 Angle : 0.585 8.393 18856 Z= 0.298 Chirality : 0.044 0.176 2060 Planarity : 0.004 0.038 2442 Dihedral : 4.105 16.558 1848 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.24 % Allowed : 22.91 % Favored : 72.85 % 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 aren not related in a simple way. whole: 0.72 (0.21), residues: 1648 helix: 0.73 (0.17), residues: 888 sheet: -1.22 (0.58), residues: 72 loop : 0.58 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 136 TYR 0.021 0.002 TYR B 77 PHE 0.018 0.002 PHE A 730 TRP 0.008 0.002 TRP B 139 HIS 0.004 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00606 (13948) covalent geometry : angle 0.57305 (18832) hydrogen bonds : bond 0.04830 ( 656) hydrogen bonds : angle 5.01523 ( 1848) metal coordination : bond 0.00769 ( 16) metal coordination : angle 3.40232 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 379 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 130 GLN cc_start: 0.8364 (mt0) cc_final: 0.8050 (mt0) REVERT: C 132 LYS cc_start: 0.7775 (tppt) cc_final: 0.7501 (tppp) REVERT: C 294 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7327 (ptm-80) REVERT: C 323 LYS cc_start: 0.8387 (mtpm) cc_final: 0.8172 (mtpp) REVERT: C 327 LEU cc_start: 0.8482 (tt) cc_final: 0.8254 (mt) REVERT: C 338 ARG cc_start: 0.8126 (mtt-85) cc_final: 0.7801 (mtp85) REVERT: C 355 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: C 447 GLU cc_start: 0.7246 (pp20) cc_final: 0.7008 (pm20) REVERT: C 462 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8113 (mtmt) REVERT: C 558 GLU cc_start: 0.7548 (pm20) cc_final: 0.7214 (pm20) REVERT: C 576 GLN cc_start: 0.8300 (tt0) cc_final: 0.8044 (tt0) REVERT: C 593 ASP cc_start: 0.7341 (t0) cc_final: 0.7132 (t0) REVERT: C 595 SER cc_start: 0.8323 (p) cc_final: 0.8065 (m) REVERT: C 692 MET cc_start: 0.6889 (mmm) cc_final: 0.6484 (mmm) REVERT: C 693 MET cc_start: 0.7193 (mtt) cc_final: 0.6729 (mtt) REVERT: C 762 SER cc_start: 0.7694 (OUTLIER) cc_final: 0.7477 (p) REVERT: C 783 ASP cc_start: 0.7609 (m-30) cc_final: 0.7382 (m-30) REVERT: C 825 MET cc_start: 0.8635 (ttm) cc_final: 0.8347 (ttt) REVERT: C 829 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8622 (ttmt) REVERT: B 17 ARG cc_start: 0.7406 (ptm-80) cc_final: 0.7049 (ptm-80) REVERT: B 18 LYS cc_start: 0.8624 (mptp) cc_final: 0.8415 (mmtm) REVERT: B 99 TYR cc_start: 0.8682 (m-80) cc_final: 0.8402 (m-80) REVERT: B 130 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: B 131 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8265 (mtt180) REVERT: B 142 ARG cc_start: 0.8577 (tpp80) cc_final: 0.8332 (tpp-160) REVERT: A 128 LEU cc_start: 0.8332 (mp) cc_final: 0.8108 (mm) REVERT: A 132 LYS cc_start: 0.7770 (tppt) cc_final: 0.7479 (tptp) REVERT: A 161 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6304 (pm20) REVERT: A 165 GLN cc_start: 0.7913 (mp10) cc_final: 0.7516 (mp10) REVERT: A 338 ARG cc_start: 0.7936 (mtp85) cc_final: 0.7622 (mtp85) REVERT: A 355 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: A 447 GLU cc_start: 0.7465 (mp0) cc_final: 0.7153 (mp0) REVERT: A 460 MET cc_start: 0.8805 (mmm) cc_final: 0.8443 (mmt) REVERT: A 526 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7905 (ttpp) REVERT: A 542 MET cc_start: 0.7633 (tpp) cc_final: 0.7234 (tpp) REVERT: A 558 GLU cc_start: 0.7531 (pm20) cc_final: 0.7270 (pm20) REVERT: A 593 ASP cc_start: 0.7290 (t0) cc_final: 0.6861 (t0) REVERT: A 605 SER cc_start: 0.8023 (t) cc_final: 0.7722 (p) REVERT: A 663 LYS cc_start: 0.7971 (ptmm) cc_final: 0.7582 (ttpp) REVERT: A 667 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7362 (pm20) REVERT: A 692 MET cc_start: 0.6824 (mmm) cc_final: 0.6347 (mmm) REVERT: A 693 MET cc_start: 0.7102 (mtt) cc_final: 0.6762 (mtt) REVERT: A 743 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7617 (mm-30) REVERT: A 783 ASP cc_start: 0.7626 (m-30) cc_final: 0.7392 (m-30) outliers start: 65 outliers final: 26 residues processed: 402 average time/residue: 0.7704 time to fit residues: 333.0189 Evaluate side-chains 410 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 374 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 731 LYS Chi-restraints excluded: chain C residue 762 SER Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 829 LYS Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 764 ASN Chi-restraints excluded: chain A residue 812 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 101 optimal weight: 0.0270 chunk 91 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN C 517 GLN C 602 ASN C 626 ASN B 43 GLN B 112 ASN A 473 ASN A 626 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.145202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124376 restraints weight = 18334.199| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.72 r_work: 0.3470 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13964 Z= 0.132 Angle : 0.499 8.760 18856 Z= 0.255 Chirality : 0.039 0.124 2060 Planarity : 0.003 0.034 2442 Dihedral : 3.866 16.169 1846 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.79 % Allowed : 24.35 % Favored : 71.87 % 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 aren not related in a simple way. whole: 1.00 (0.21), residues: 1648 helix: 1.05 (0.17), residues: 892 sheet: -1.51 (0.56), residues: 72 loop : 0.62 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 136 TYR 0.014 0.001 TYR D 77 PHE 0.010 0.001 PHE C 733 TRP 0.008 0.001 TRP B 139 HIS 0.002 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00308 (13948) covalent geometry : angle 0.48890 (18832) hydrogen bonds : bond 0.03878 ( 656) hydrogen bonds : angle 4.70600 ( 1848) metal coordination : bond 0.00367 ( 16) metal coordination : angle 2.78820 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 376 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 18 LYS cc_start: 0.8784 (mmtp) cc_final: 0.8533 (tptt) REVERT: D 55 ARG cc_start: 0.8597 (mtm-85) cc_final: 0.8392 (mtt90) REVERT: C 132 LYS cc_start: 0.7795 (tppt) cc_final: 0.7575 (tppp) REVERT: C 268 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6990 (tt0) REVERT: C 311 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8381 (mttp) REVERT: C 323 LYS cc_start: 0.8358 (mtpm) cc_final: 0.8155 (mtpp) REVERT: C 327 LEU cc_start: 0.8520 (tt) cc_final: 0.8289 (mt) REVERT: C 355 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: C 447 GLU cc_start: 0.7077 (pp20) cc_final: 0.6824 (pm20) REVERT: C 593 ASP cc_start: 0.7289 (t0) cc_final: 0.6974 (t0) REVERT: C 611 GLN cc_start: 0.8181 (mp10) cc_final: 0.7919 (mt0) REVERT: C 663 LYS cc_start: 0.7837 (ttpp) cc_final: 0.7434 (ttpp) REVERT: C 676 MET cc_start: 0.7223 (mtm) cc_final: 0.7011 (mpt) REVERT: C 692 MET cc_start: 0.6869 (mmm) cc_final: 0.6478 (mmm) REVERT: C 693 MET cc_start: 0.7033 (mtt) cc_final: 0.6573 (mtt) REVERT: C 703 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8087 (tt) REVERT: C 783 ASP cc_start: 0.7513 (m-30) cc_final: 0.7292 (m-30) REVERT: C 807 GLN cc_start: 0.8394 (tp-100) cc_final: 0.8177 (tp40) REVERT: C 825 MET cc_start: 0.8636 (ttm) cc_final: 0.8351 (ttt) REVERT: B 17 ARG cc_start: 0.7395 (ptm-80) cc_final: 0.7018 (ptm-80) REVERT: B 130 GLN cc_start: 0.8233 (mt0) cc_final: 0.7957 (mt0) REVERT: B 131 ARG cc_start: 0.8682 (mtm-85) cc_final: 0.8132 (mtt-85) REVERT: B 136 ARG cc_start: 0.8115 (mmm-85) cc_final: 0.7568 (mmm-85) REVERT: A 132 LYS cc_start: 0.7817 (tppt) cc_final: 0.7513 (tptp) REVERT: A 165 GLN cc_start: 0.7893 (mp10) cc_final: 0.7285 (mp-120) REVERT: A 338 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7608 (mtp85) REVERT: A 355 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6968 (tm-30) REVERT: A 447 GLU cc_start: 0.7401 (mp0) cc_final: 0.7079 (mp0) REVERT: A 526 LYS cc_start: 0.8334 (tppp) cc_final: 0.7872 (ttpp) REVERT: A 542 MET cc_start: 0.7591 (tpp) cc_final: 0.7258 (tpp) REVERT: A 558 GLU cc_start: 0.7446 (pm20) cc_final: 0.7205 (pm20) REVERT: A 593 ASP cc_start: 0.7248 (t0) cc_final: 0.7036 (t0) REVERT: A 605 SER cc_start: 0.8030 (t) cc_final: 0.7771 (p) REVERT: A 663 LYS cc_start: 0.7964 (ptmm) cc_final: 0.7679 (ttpp) REVERT: A 667 GLU cc_start: 0.7747 (pm20) cc_final: 0.7370 (pm20) REVERT: A 692 MET cc_start: 0.6850 (mmm) cc_final: 0.6396 (mmm) REVERT: A 693 MET cc_start: 0.7146 (mtt) cc_final: 0.6797 (mtt) REVERT: A 743 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7651 (mm-30) REVERT: A 771 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: A 851 GLU cc_start: 0.7929 (tt0) cc_final: 0.7629 (tt0) outliers start: 58 outliers final: 28 residues processed: 394 average time/residue: 0.7950 time to fit residues: 337.2391 Evaluate side-chains 398 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 365 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 731 LYS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 771 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 141 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN C 517 GLN C 626 ASN C 807 GLN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 ASN A 626 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.146176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124692 restraints weight = 17954.097| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.76 r_work: 0.3454 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13964 Z= 0.160 Angle : 0.510 7.821 18856 Z= 0.259 Chirality : 0.040 0.125 2060 Planarity : 0.003 0.033 2442 Dihedral : 3.841 16.458 1846 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.44 % Allowed : 23.04 % Favored : 72.52 % 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 aren not related in a simple way. whole: 1.10 (0.21), residues: 1648 helix: 1.18 (0.18), residues: 888 sheet: -1.52 (0.57), residues: 72 loop : 0.59 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 338 TYR 0.017 0.001 TYR B 77 PHE 0.012 0.001 PHE A 730 TRP 0.007 0.001 TRP B 139 HIS 0.002 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00378 (13948) covalent geometry : angle 0.50151 (18832) hydrogen bonds : bond 0.03875 ( 656) hydrogen bonds : angle 4.58946 ( 1848) metal coordination : bond 0.00455 ( 16) metal coordination : angle 2.65606 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 375 time to evaluate : 0.501 Fit side-chains REVERT: D 18 LYS cc_start: 0.8832 (mmtp) cc_final: 0.8578 (tptt) REVERT: C 132 LYS cc_start: 0.7836 (tppt) cc_final: 0.7590 (tppp) REVERT: C 264 SER cc_start: 0.7985 (m) cc_final: 0.7741 (t) REVERT: C 268 GLU cc_start: 0.7264 (tt0) cc_final: 0.6920 (tp30) REVERT: C 311 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8316 (mttp) REVERT: C 327 LEU cc_start: 0.8527 (tt) cc_final: 0.8286 (mt) REVERT: C 355 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: C 447 GLU cc_start: 0.7146 (pp20) cc_final: 0.6904 (pm20) REVERT: C 593 ASP cc_start: 0.7312 (t0) cc_final: 0.7056 (t0) REVERT: C 663 LYS cc_start: 0.7920 (ttpp) cc_final: 0.7598 (ttpp) REVERT: C 666 LEU cc_start: 0.8102 (tp) cc_final: 0.7879 (mt) REVERT: C 676 MET cc_start: 0.7293 (mtm) cc_final: 0.7087 (mpt) REVERT: C 692 MET cc_start: 0.6910 (mmm) cc_final: 0.6503 (mmm) REVERT: C 693 MET cc_start: 0.7151 (mtt) cc_final: 0.6773 (mtt) REVERT: C 703 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8117 (tt) REVERT: C 739 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8220 (ptm) REVERT: C 825 MET cc_start: 0.8640 (ttm) cc_final: 0.8370 (ttt) REVERT: C 829 LYS cc_start: 0.8826 (tttm) cc_final: 0.8598 (ttmt) REVERT: B 17 ARG cc_start: 0.7457 (ptm-80) cc_final: 0.7038 (ptm-80) REVERT: B 130 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7970 (mt0) REVERT: B 131 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8191 (mtm-85) REVERT: B 136 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7549 (mmm-85) REVERT: A 132 LYS cc_start: 0.7809 (tppt) cc_final: 0.7503 (tptp) REVERT: A 165 GLN cc_start: 0.7938 (mp10) cc_final: 0.7381 (mp-120) REVERT: A 323 LYS cc_start: 0.8237 (mtpm) cc_final: 0.7971 (ttpp) REVERT: A 338 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7556 (mtp85) REVERT: A 355 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: A 435 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7496 (mtpt) REVERT: A 447 GLU cc_start: 0.7439 (mp0) cc_final: 0.7102 (mp0) REVERT: A 542 MET cc_start: 0.7625 (tpp) cc_final: 0.7327 (tpp) REVERT: A 558 GLU cc_start: 0.7435 (pm20) cc_final: 0.7227 (pm20) REVERT: A 605 SER cc_start: 0.8043 (t) cc_final: 0.7798 (p) REVERT: A 663 LYS cc_start: 0.7972 (ptmm) cc_final: 0.7641 (ttpp) REVERT: A 667 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7383 (pm20) REVERT: A 692 MET cc_start: 0.6896 (mmm) cc_final: 0.6411 (mmm) REVERT: A 693 MET cc_start: 0.7142 (mtt) cc_final: 0.6806 (mtt) REVERT: A 743 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7612 (mm-30) REVERT: A 772 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7471 (mp0) REVERT: A 782 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7267 (mtm-85) outliers start: 68 outliers final: 36 residues processed: 396 average time/residue: 0.7972 time to fit residues: 338.8115 Evaluate side-chains 410 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 366 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 747 LYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 747 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 108 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 101 optimal weight: 0.0470 chunk 159 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN C 517 GLN C 626 ASN C 807 GLN B 112 ASN A 626 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.145190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124308 restraints weight = 18315.134| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.74 r_work: 0.3472 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13964 Z= 0.119 Angle : 0.489 7.931 18856 Z= 0.246 Chirality : 0.039 0.178 2060 Planarity : 0.003 0.040 2442 Dihedral : 3.714 15.658 1846 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.59 % Allowed : 24.28 % Favored : 72.13 % 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 aren not related in a simple way. whole: 1.25 (0.21), residues: 1648 helix: 1.34 (0.18), residues: 888 sheet: -1.44 (0.58), residues: 72 loop : 0.60 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 136 TYR 0.013 0.001 TYR D 77 PHE 0.010 0.001 PHE C 733 TRP 0.007 0.001 TRP B 139 HIS 0.002 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00278 (13948) covalent geometry : angle 0.47972 (18832) hydrogen bonds : bond 0.03475 ( 656) hydrogen bonds : angle 4.43738 ( 1848) metal coordination : bond 0.00347 ( 16) metal coordination : angle 2.73662 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 374 time to evaluate : 0.522 Fit side-chains REVERT: D 18 LYS cc_start: 0.8815 (mmtp) cc_final: 0.8595 (tptt) REVERT: D 131 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8327 (mtt180) REVERT: D 142 ARG cc_start: 0.8519 (tpp80) cc_final: 0.8248 (tpp80) REVERT: C 138 GLU cc_start: 0.6848 (pp20) cc_final: 0.6625 (pp20) REVERT: C 264 SER cc_start: 0.7965 (m) cc_final: 0.7708 (t) REVERT: C 268 GLU cc_start: 0.7257 (tt0) cc_final: 0.6928 (tp30) REVERT: C 311 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8264 (mttp) REVERT: C 327 LEU cc_start: 0.8468 (tt) cc_final: 0.8250 (mt) REVERT: C 338 ARG cc_start: 0.7992 (ttt-90) cc_final: 0.7760 (ttm-80) REVERT: C 355 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: C 447 GLU cc_start: 0.7108 (pp20) cc_final: 0.6898 (pm20) REVERT: C 593 ASP cc_start: 0.7288 (t0) cc_final: 0.7026 (t0) REVERT: C 676 MET cc_start: 0.7299 (mtm) cc_final: 0.6961 (mpt) REVERT: C 692 MET cc_start: 0.6952 (mmm) cc_final: 0.6524 (mmm) REVERT: C 693 MET cc_start: 0.7095 (mtt) cc_final: 0.6852 (mtt) REVERT: C 825 MET cc_start: 0.8607 (ttm) cc_final: 0.8357 (ttt) REVERT: C 829 LYS cc_start: 0.8805 (tttm) cc_final: 0.8593 (ttmt) REVERT: B 17 ARG cc_start: 0.7438 (ptm-80) cc_final: 0.7006 (ptm-80) REVERT: B 130 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: B 131 ARG cc_start: 0.8668 (mtm-85) cc_final: 0.8199 (mtm-85) REVERT: A 132 LYS cc_start: 0.7861 (tppt) cc_final: 0.7549 (tptp) REVERT: A 137 LEU cc_start: 0.8450 (tp) cc_final: 0.8244 (tt) REVERT: A 165 GLN cc_start: 0.7922 (mp10) cc_final: 0.7307 (mp-120) REVERT: A 323 LYS cc_start: 0.8213 (mtpm) cc_final: 0.7991 (ttpp) REVERT: A 338 ARG cc_start: 0.7777 (mtp85) cc_final: 0.7460 (mtp85) REVERT: A 355 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6838 (tm-30) REVERT: A 447 GLU cc_start: 0.7381 (mp0) cc_final: 0.7021 (mp0) REVERT: A 605 SER cc_start: 0.8081 (t) cc_final: 0.7827 (p) REVERT: A 663 LYS cc_start: 0.7951 (ptmm) cc_final: 0.7614 (ttpp) REVERT: A 667 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: A 692 MET cc_start: 0.6888 (mmm) cc_final: 0.6405 (mmm) REVERT: A 693 MET cc_start: 0.7136 (mtt) cc_final: 0.6795 (mtt) REVERT: A 743 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7558 (mm-30) REVERT: A 770 LEU cc_start: 0.8196 (tp) cc_final: 0.7986 (tt) REVERT: A 782 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.7233 (mtm-85) outliers start: 55 outliers final: 23 residues processed: 387 average time/residue: 0.7197 time to fit residues: 298.8300 Evaluate side-chains 388 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 360 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 747 LYS Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 747 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 147 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN C 354 ASN C 517 GLN C 626 ASN C 807 GLN A 626 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.146585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125086 restraints weight = 17916.655| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.77 r_work: 0.3462 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13964 Z= 0.140 Angle : 0.504 8.630 18856 Z= 0.254 Chirality : 0.040 0.168 2060 Planarity : 0.003 0.036 2442 Dihedral : 3.735 15.471 1846 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.52 % Allowed : 24.54 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.21), residues: 1648 helix: 1.34 (0.18), residues: 888 sheet: -1.48 (0.57), residues: 72 loop : 0.61 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 735 TYR 0.015 0.001 TYR B 77 PHE 0.010 0.001 PHE A 730 TRP 0.007 0.001 TRP B 139 HIS 0.002 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00331 (13948) covalent geometry : angle 0.49604 (18832) hydrogen bonds : bond 0.03607 ( 656) hydrogen bonds : angle 4.41739 ( 1848) metal coordination : bond 0.00429 ( 16) metal coordination : angle 2.57018 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 364 time to evaluate : 0.630 Fit side-chains REVERT: D 18 LYS cc_start: 0.8808 (mmtp) cc_final: 0.8593 (tptt) REVERT: D 142 ARG cc_start: 0.8559 (tpp80) cc_final: 0.8308 (tpp80) REVERT: C 138 GLU cc_start: 0.6876 (pp20) cc_final: 0.6620 (pp20) REVERT: C 264 SER cc_start: 0.7980 (m) cc_final: 0.7724 (t) REVERT: C 268 GLU cc_start: 0.7239 (tt0) cc_final: 0.6786 (tp30) REVERT: C 311 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8167 (mttp) REVERT: C 327 LEU cc_start: 0.8483 (tt) cc_final: 0.8253 (mt) REVERT: C 339 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8250 (mtm) REVERT: C 355 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: C 447 GLU cc_start: 0.7131 (pp20) cc_final: 0.6927 (pm20) REVERT: C 524 ARG cc_start: 0.8071 (tpp80) cc_final: 0.7825 (tpt170) REVERT: C 593 ASP cc_start: 0.7246 (t0) cc_final: 0.7025 (t0) REVERT: C 676 MET cc_start: 0.7303 (mtm) cc_final: 0.6974 (mpt) REVERT: C 692 MET cc_start: 0.7008 (mmm) cc_final: 0.6581 (mmm) REVERT: C 693 MET cc_start: 0.7113 (mtt) cc_final: 0.6842 (mtt) REVERT: C 825 MET cc_start: 0.8577 (ttm) cc_final: 0.8303 (ttt) REVERT: C 829 LYS cc_start: 0.8805 (tttm) cc_final: 0.8591 (ttmt) REVERT: B 17 ARG cc_start: 0.7456 (ptm-80) cc_final: 0.7057 (ptm-80) REVERT: B 131 ARG cc_start: 0.8670 (mtm-85) cc_final: 0.8194 (mtm-85) REVERT: A 132 LYS cc_start: 0.7870 (tppt) cc_final: 0.7552 (tptp) REVERT: A 137 LEU cc_start: 0.8453 (tp) cc_final: 0.8242 (tt) REVERT: A 165 GLN cc_start: 0.7953 (mp10) cc_final: 0.7549 (mp-120) REVERT: A 338 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7543 (mtp85) REVERT: A 339 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8142 (mtm) REVERT: A 355 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6844 (tm-30) REVERT: A 447 GLU cc_start: 0.7371 (mp0) cc_final: 0.7012 (mp0) REVERT: A 605 SER cc_start: 0.8040 (t) cc_final: 0.7817 (p) REVERT: A 663 LYS cc_start: 0.7992 (ptmm) cc_final: 0.7613 (ttpp) REVERT: A 667 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7352 (pm20) REVERT: A 692 MET cc_start: 0.6966 (mmm) cc_final: 0.6459 (mmm) REVERT: A 693 MET cc_start: 0.7191 (mtt) cc_final: 0.6907 (mtt) REVERT: A 743 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7577 (mm-30) REVERT: A 770 LEU cc_start: 0.8247 (tp) cc_final: 0.8041 (tt) REVERT: A 782 ARG cc_start: 0.7432 (ttm-80) cc_final: 0.7212 (mtm-85) outliers start: 54 outliers final: 36 residues processed: 380 average time/residue: 0.7136 time to fit residues: 291.4218 Evaluate side-chains 400 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 358 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 649 ARG Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 721 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 116 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN C 393 ASN C 517 GLN C 626 ASN C 764 ASN C 807 GLN A 626 ASN A 764 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.145346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.123524 restraints weight = 17860.922| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.77 r_work: 0.3442 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13964 Z= 0.213 Angle : 0.557 9.232 18856 Z= 0.279 Chirality : 0.042 0.174 2060 Planarity : 0.004 0.036 2442 Dihedral : 3.934 16.436 1846 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.85 % Allowed : 24.80 % Favored : 71.34 % 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 aren not related in a simple way. whole: 1.06 (0.21), residues: 1648 helix: 1.14 (0.18), residues: 888 sheet: -1.42 (0.58), residues: 72 loop : 0.56 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 539 TYR 0.020 0.002 TYR B 77 PHE 0.015 0.002 PHE A 730 TRP 0.007 0.002 TRP B 139 HIS 0.005 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00507 (13948) covalent geometry : angle 0.54771 (18832) hydrogen bonds : bond 0.04089 ( 656) hydrogen bonds : angle 4.56543 ( 1848) metal coordination : bond 0.00677 ( 16) metal coordination : angle 2.96260 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 369 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: D 18 LYS cc_start: 0.8813 (mmtp) cc_final: 0.8573 (tptt) REVERT: C 129 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7756 (p) REVERT: C 138 GLU cc_start: 0.6908 (pp20) cc_final: 0.6640 (pp20) REVERT: C 264 SER cc_start: 0.7987 (m) cc_final: 0.7770 (m) REVERT: C 268 GLU cc_start: 0.7264 (tt0) cc_final: 0.6905 (tp30) REVERT: C 311 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8332 (mttp) REVERT: C 327 LEU cc_start: 0.8493 (tt) cc_final: 0.8257 (mt) REVERT: C 339 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8305 (mtm) REVERT: C 355 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: C 593 ASP cc_start: 0.7317 (t0) cc_final: 0.7087 (t0) REVERT: C 676 MET cc_start: 0.7240 (mtm) cc_final: 0.6836 (mpt) REVERT: C 692 MET cc_start: 0.7026 (mmm) cc_final: 0.6630 (mmm) REVERT: C 693 MET cc_start: 0.7130 (mtt) cc_final: 0.6874 (mtt) REVERT: C 825 MET cc_start: 0.8666 (ttm) cc_final: 0.8392 (ttt) REVERT: C 829 LYS cc_start: 0.8827 (tttm) cc_final: 0.8598 (ttmt) REVERT: C 856 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: B 17 ARG cc_start: 0.7485 (ptm-80) cc_final: 0.7103 (ptm-80) REVERT: B 131 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8172 (mtm-85) REVERT: A 132 LYS cc_start: 0.7872 (tppt) cc_final: 0.7542 (tptp) REVERT: A 137 LEU cc_start: 0.8437 (tp) cc_final: 0.8222 (tt) REVERT: A 165 GLN cc_start: 0.7960 (mp10) cc_final: 0.7676 (mp-120) REVERT: A 338 ARG cc_start: 0.7852 (mtp85) cc_final: 0.7481 (mtp85) REVERT: A 339 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8139 (mtm) REVERT: A 341 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 355 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: A 447 GLU cc_start: 0.7511 (mp0) cc_final: 0.7124 (mp0) REVERT: A 605 SER cc_start: 0.8075 (t) cc_final: 0.7830 (p) REVERT: A 663 LYS cc_start: 0.7999 (ptmm) cc_final: 0.7652 (ttpp) REVERT: A 667 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: A 692 MET cc_start: 0.6985 (mmm) cc_final: 0.6476 (mmm) REVERT: A 693 MET cc_start: 0.7274 (mtt) cc_final: 0.6980 (mtt) REVERT: A 743 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7600 (mm-30) outliers start: 59 outliers final: 37 residues processed: 390 average time/residue: 0.6719 time to fit residues: 281.6059 Evaluate side-chains 408 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 363 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 649 ARG Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 856 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 747 LYS Chi-restraints excluded: chain A residue 764 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 51 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 129 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN C 517 GLN C 626 ASN C 807 GLN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN A 764 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.146304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124779 restraints weight = 17828.685| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.76 r_work: 0.3458 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13964 Z= 0.160 Angle : 0.536 10.042 18856 Z= 0.269 Chirality : 0.041 0.154 2060 Planarity : 0.003 0.032 2442 Dihedral : 3.873 15.966 1846 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.33 % Allowed : 25.20 % Favored : 71.48 % 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 aren not related in a simple way. whole: 1.12 (0.21), residues: 1648 helix: 1.23 (0.18), residues: 888 sheet: -1.41 (0.58), residues: 72 loop : 0.53 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 338 TYR 0.016 0.001 TYR D 77 PHE 0.012 0.001 PHE B 76 TRP 0.007 0.001 TRP B 139 HIS 0.002 0.001 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00382 (13948) covalent geometry : angle 0.52742 (18832) hydrogen bonds : bond 0.03781 ( 656) hydrogen bonds : angle 4.47998 ( 1848) metal coordination : bond 0.00543 ( 16) metal coordination : angle 2.80207 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 366 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: D 18 LYS cc_start: 0.8824 (mmtp) cc_final: 0.8574 (tptt) REVERT: C 129 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7606 (p) REVERT: C 138 GLU cc_start: 0.6917 (pp20) cc_final: 0.6639 (pp20) REVERT: C 264 SER cc_start: 0.7969 (m) cc_final: 0.7752 (m) REVERT: C 268 GLU cc_start: 0.7239 (tt0) cc_final: 0.6906 (tp30) REVERT: C 311 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8247 (mttp) REVERT: C 327 LEU cc_start: 0.8477 (tt) cc_final: 0.8256 (mt) REVERT: C 339 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8296 (mtm) REVERT: C 355 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: C 447 GLU cc_start: 0.7095 (pp20) cc_final: 0.6889 (pm20) REVERT: C 593 ASP cc_start: 0.7289 (t0) cc_final: 0.7063 (t0) REVERT: C 597 LYS cc_start: 0.8479 (mttm) cc_final: 0.8242 (mtpp) REVERT: C 676 MET cc_start: 0.7220 (mtm) cc_final: 0.6821 (mpt) REVERT: C 692 MET cc_start: 0.6973 (mmm) cc_final: 0.6592 (mmm) REVERT: C 693 MET cc_start: 0.7092 (mtt) cc_final: 0.6847 (mtt) REVERT: C 825 MET cc_start: 0.8648 (ttm) cc_final: 0.8323 (ttt) REVERT: B 17 ARG cc_start: 0.7466 (ptm-80) cc_final: 0.7092 (ptm-80) REVERT: B 131 ARG cc_start: 0.8700 (mtm-85) cc_final: 0.8198 (mtm-85) REVERT: B 142 ARG cc_start: 0.8563 (tpp80) cc_final: 0.8339 (tpp-160) REVERT: A 132 LYS cc_start: 0.7882 (tppt) cc_final: 0.7517 (tptp) REVERT: A 137 LEU cc_start: 0.8443 (tp) cc_final: 0.8228 (tt) REVERT: A 165 GLN cc_start: 0.7959 (mp10) cc_final: 0.7668 (mp-120) REVERT: A 338 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7532 (mtp85) REVERT: A 339 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8147 (mtm) REVERT: A 341 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7835 (mt-10) REVERT: A 355 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: A 447 GLU cc_start: 0.7500 (mp0) cc_final: 0.7107 (mp0) REVERT: A 605 SER cc_start: 0.8069 (t) cc_final: 0.7841 (p) REVERT: A 663 LYS cc_start: 0.8003 (ptmm) cc_final: 0.7659 (ttpp) REVERT: A 667 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: A 692 MET cc_start: 0.6975 (mmm) cc_final: 0.6510 (mmm) REVERT: A 693 MET cc_start: 0.7235 (mtt) cc_final: 0.6946 (mtt) REVERT: A 743 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7629 (mm-30) outliers start: 51 outliers final: 34 residues processed: 390 average time/residue: 0.7497 time to fit residues: 314.6148 Evaluate side-chains 401 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 360 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 649 ARG Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 764 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 154 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 111 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN C 517 GLN C 626 ASN C 807 GLN C 841 HIS ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN A 841 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.147156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125621 restraints weight = 17968.305| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.77 r_work: 0.3465 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13964 Z= 0.141 Angle : 0.541 10.899 18856 Z= 0.268 Chirality : 0.040 0.154 2060 Planarity : 0.003 0.031 2442 Dihedral : 3.833 15.717 1846 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.13 % Allowed : 25.91 % Favored : 70.95 % 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 aren not related in a simple way. whole: 1.14 (0.21), residues: 1648 helix: 1.25 (0.18), residues: 892 sheet: -1.47 (0.58), residues: 72 loop : 0.54 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 763 TYR 0.015 0.001 TYR D 77 PHE 0.013 0.001 PHE B 76 TRP 0.007 0.001 TRP B 139 HIS 0.003 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00337 (13948) covalent geometry : angle 0.53218 (18832) hydrogen bonds : bond 0.03632 ( 656) hydrogen bonds : angle 4.44444 ( 1848) metal coordination : bond 0.00443 ( 16) metal coordination : angle 2.74627 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 361 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: D 18 LYS cc_start: 0.8847 (mmtp) cc_final: 0.8596 (tptt) REVERT: D 131 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8301 (mtt180) REVERT: C 129 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7562 (p) REVERT: C 132 LYS cc_start: 0.7860 (tppp) cc_final: 0.7601 (tppp) REVERT: C 138 GLU cc_start: 0.6923 (pp20) cc_final: 0.6624 (pp20) REVERT: C 264 SER cc_start: 0.7964 (m) cc_final: 0.7739 (m) REVERT: C 268 GLU cc_start: 0.7212 (tt0) cc_final: 0.6817 (tp30) REVERT: C 311 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8148 (mttp) REVERT: C 327 LEU cc_start: 0.8465 (tt) cc_final: 0.8245 (mt) REVERT: C 339 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8276 (mtm) REVERT: C 355 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: C 447 GLU cc_start: 0.7094 (pp20) cc_final: 0.6882 (pm20) REVERT: C 593 ASP cc_start: 0.7261 (t0) cc_final: 0.7039 (t0) REVERT: C 597 LYS cc_start: 0.8476 (mttm) cc_final: 0.8241 (mtpp) REVERT: C 611 GLN cc_start: 0.8181 (mp10) cc_final: 0.7965 (mt0) REVERT: C 692 MET cc_start: 0.6939 (mmm) cc_final: 0.6568 (mmm) REVERT: C 693 MET cc_start: 0.7071 (mtt) cc_final: 0.6810 (mtt) REVERT: C 825 MET cc_start: 0.8647 (ttm) cc_final: 0.8338 (ttt) REVERT: B 17 ARG cc_start: 0.7469 (ptm-80) cc_final: 0.7160 (ptm-80) REVERT: B 130 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: B 131 ARG cc_start: 0.8694 (mtm-85) cc_final: 0.8198 (mtm-85) REVERT: A 132 LYS cc_start: 0.7875 (tppt) cc_final: 0.7509 (tptp) REVERT: A 165 GLN cc_start: 0.7943 (mp10) cc_final: 0.7690 (mp-120) REVERT: A 338 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7553 (mtp85) REVERT: A 339 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8147 (mtm) REVERT: A 341 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7821 (mt-10) REVERT: A 355 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6854 (tm-30) REVERT: A 447 GLU cc_start: 0.7428 (mp0) cc_final: 0.7051 (mp0) REVERT: A 605 SER cc_start: 0.8056 (t) cc_final: 0.7839 (p) REVERT: A 663 LYS cc_start: 0.8006 (ptmm) cc_final: 0.7664 (ttpp) REVERT: A 667 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7381 (pm20) REVERT: A 692 MET cc_start: 0.6978 (mmm) cc_final: 0.6521 (mmm) REVERT: A 693 MET cc_start: 0.7240 (mtt) cc_final: 0.6954 (mtt) REVERT: A 743 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7606 (mm-30) outliers start: 48 outliers final: 33 residues processed: 382 average time/residue: 0.8038 time to fit residues: 329.1504 Evaluate side-chains 400 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 359 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 649 ARG Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 721 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 35 optimal weight: 0.0030 chunk 132 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 64 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C 626 ASN C 841 HIS ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN A 841 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.147521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126024 restraints weight = 17838.078| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.76 r_work: 0.3476 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13964 Z= 0.121 Angle : 0.537 10.918 18856 Z= 0.265 Chirality : 0.040 0.147 2060 Planarity : 0.003 0.034 2442 Dihedral : 3.779 14.797 1846 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.81 % Allowed : 26.44 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.21), residues: 1648 helix: 1.36 (0.18), residues: 890 sheet: -1.48 (0.57), residues: 72 loop : 0.56 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 539 TYR 0.015 0.001 TYR A 502 PHE 0.013 0.001 PHE B 76 TRP 0.007 0.001 TRP B 139 HIS 0.002 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00287 (13948) covalent geometry : angle 0.52859 (18832) hydrogen bonds : bond 0.03488 ( 656) hydrogen bonds : angle 4.39362 ( 1848) metal coordination : bond 0.00377 ( 16) metal coordination : angle 2.75259 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 351 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: D 18 LYS cc_start: 0.8844 (mmtp) cc_final: 0.8616 (tptt) REVERT: D 131 ARG cc_start: 0.8698 (mtm-85) cc_final: 0.8324 (mtt180) REVERT: C 129 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7510 (p) REVERT: C 132 LYS cc_start: 0.7825 (tppp) cc_final: 0.7411 (tppp) REVERT: C 138 GLU cc_start: 0.6913 (pp20) cc_final: 0.6608 (pp20) REVERT: C 264 SER cc_start: 0.7864 (m) cc_final: 0.7631 (m) REVERT: C 268 GLU cc_start: 0.7185 (tt0) cc_final: 0.6733 (tp30) REVERT: C 311 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8144 (mttp) REVERT: C 327 LEU cc_start: 0.8458 (tt) cc_final: 0.8232 (mt) REVERT: C 339 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8267 (mtm) REVERT: C 355 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: C 593 ASP cc_start: 0.7246 (t0) cc_final: 0.7037 (t0) REVERT: C 597 LYS cc_start: 0.8467 (mttm) cc_final: 0.8238 (mtpp) REVERT: C 692 MET cc_start: 0.6953 (mmm) cc_final: 0.6582 (mmm) REVERT: C 693 MET cc_start: 0.7005 (mtt) cc_final: 0.6746 (mtt) REVERT: C 825 MET cc_start: 0.8628 (ttm) cc_final: 0.8351 (ttt) REVERT: B 17 ARG cc_start: 0.7474 (ptm-80) cc_final: 0.7158 (ptm-80) REVERT: B 130 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7937 (mt0) REVERT: B 131 ARG cc_start: 0.8682 (mtm-85) cc_final: 0.8207 (mtm-85) REVERT: A 132 LYS cc_start: 0.7872 (tppt) cc_final: 0.7519 (tptp) REVERT: A 165 GLN cc_start: 0.7955 (mp10) cc_final: 0.7641 (mp-120) REVERT: A 323 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7989 (ttpp) REVERT: A 338 ARG cc_start: 0.7821 (mtp85) cc_final: 0.7505 (mtp85) REVERT: A 339 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8130 (mtm) REVERT: A 355 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: A 447 GLU cc_start: 0.7497 (mp0) cc_final: 0.7113 (mp0) REVERT: A 605 SER cc_start: 0.8100 (t) cc_final: 0.7861 (p) REVERT: A 663 LYS cc_start: 0.7980 (ptmm) cc_final: 0.7648 (ttpp) REVERT: A 667 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7379 (pm20) REVERT: A 692 MET cc_start: 0.7001 (mmm) cc_final: 0.6530 (mmm) REVERT: A 693 MET cc_start: 0.7181 (mtt) cc_final: 0.6885 (mtt) REVERT: A 743 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7609 (mm-30) outliers start: 43 outliers final: 29 residues processed: 366 average time/residue: 0.7284 time to fit residues: 285.8054 Evaluate side-chains 385 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 348 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 649 ARG Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 681 GLN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 721 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 45 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 123 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN C 517 GLN C 626 ASN C 841 HIS ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 ASN A 626 ASN A 764 ASN A 841 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.145496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124317 restraints weight = 18284.443| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.74 r_work: 0.3462 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13964 Z= 0.153 Angle : 0.558 11.349 18856 Z= 0.275 Chirality : 0.041 0.155 2060 Planarity : 0.003 0.031 2442 Dihedral : 3.857 15.191 1846 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.68 % Allowed : 26.89 % Favored : 70.43 % 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 aren not related in a simple way. whole: 1.18 (0.21), residues: 1648 helix: 1.30 (0.18), residues: 890 sheet: -1.42 (0.57), residues: 72 loop : 0.54 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 539 TYR 0.018 0.001 TYR A 502 PHE 0.013 0.001 PHE B 76 TRP 0.007 0.001 TRP B 139 HIS 0.003 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00367 (13948) covalent geometry : angle 0.54855 (18832) hydrogen bonds : bond 0.03698 ( 656) hydrogen bonds : angle 4.46847 ( 1848) metal coordination : bond 0.00472 ( 16) metal coordination : angle 2.91069 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6703.05 seconds wall clock time: 114 minutes 37.03 seconds (6877.03 seconds total)