Starting phenix.real_space_refine on Thu Jul 31 18:30:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jrn_36599/07_2025/8jrn_36599.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jrn_36599/07_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_36599/07_2025/8jrn_36599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jrn_36599/07_2025/8jrn_36599.map" model { file = "/net/cci-nas-00/data/ceres_data/8jrn_36599/07_2025/8jrn_36599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jrn_36599/07_2025/8jrn_36599.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.94, per 1000 atoms: 0.58 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: 3.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.53 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: 4.22 Time building geometry restraints manager: 3.76 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 34.660 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP B 139 HIS 0.003 0.001 HIS B 85 PHE 0.012 0.001 PHE A 287 TYR 0.017 0.001 TYR D 77 ARG 0.006 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.20972 ( 656) hydrogen bonds : angle 7.21062 ( 1848) metal coordination : bond 0.00331 ( 16) metal coordination : angle 2.82313 ( 24) covalent geometry : bond 0.00376 (13948) covalent geometry : angle 0.50915 (18832) *********************** 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 : 1.662 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: 1.4399 time to fit residues: 617.1511 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 : 1.699 ------------------------------------------------------------------------------- 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 138 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 49 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 148 optimal weight: 4.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 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 602 ASN C 626 ASN C 715 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 = 0.3882 r_free = 0.3882 target = 0.146995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125391 restraints weight = 17933.138| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.76 r_work: 0.3474 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13964 Z= 0.143 Angle : 0.517 8.403 18856 Z= 0.264 Chirality : 0.039 0.147 2060 Planarity : 0.003 0.036 2442 Dihedral : 3.826 15.325 1848 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.85 % Allowed : 23.04 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1648 helix: 1.06 (0.18), residues: 866 sheet: -1.28 (0.57), residues: 72 loop : 0.68 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 791 HIS 0.003 0.001 HIS C 297 PHE 0.010 0.001 PHE C 733 TYR 0.014 0.001 TYR B 77 ARG 0.004 0.000 ARG B 136 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 656) hydrogen bonds : angle 4.84874 ( 1848) metal coordination : bond 0.00418 ( 16) metal coordination : angle 2.68002 ( 24) covalent geometry : bond 0.00332 (13948) covalent geometry : angle 0.50790 (18832) *********************** 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 425 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 366 time to evaluate : 1.655 Fit side-chains revert: symmetry clash REVERT: D 130 GLN cc_start: 0.8371 (mt0) cc_final: 0.8103 (mt0) REVERT: D 131 ARG cc_start: 0.8643 (mtm-85) cc_final: 0.8188 (mtt180) REVERT: C 132 LYS cc_start: 0.7736 (tppt) cc_final: 0.7534 (tppp) REVERT: C 323 LYS cc_start: 0.8365 (mtpm) cc_final: 0.8152 (mtpp) REVERT: C 327 LEU cc_start: 0.8484 (tt) cc_final: 0.8249 (mt) REVERT: C 355 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7287 (tm-30) REVERT: C 447 GLU cc_start: 0.7070 (pp20) cc_final: 0.6826 (pm20) REVERT: C 576 GLN cc_start: 0.8282 (tt0) cc_final: 0.8068 (tt0) REVERT: C 593 ASP cc_start: 0.7222 (t0) cc_final: 0.6979 (t0) REVERT: C 611 GLN cc_start: 0.8284 (mp10) cc_final: 0.7904 (mt0) REVERT: C 692 MET cc_start: 0.6841 (mmm) cc_final: 0.6452 (mmm) REVERT: C 693 MET cc_start: 0.7129 (mtt) cc_final: 0.6718 (mtt) REVERT: C 825 MET cc_start: 0.8643 (ttm) cc_final: 0.8348 (ttt) REVERT: B 17 ARG cc_start: 0.7390 (ptm-80) cc_final: 0.7019 (ptm-80) REVERT: B 99 TYR cc_start: 0.8656 (m-80) cc_final: 0.8414 (m-80) REVERT: B 130 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7952 (mt0) REVERT: B 131 ARG cc_start: 0.8666 (mtm-85) cc_final: 0.8140 (mtt-85) REVERT: B 136 ARG cc_start: 0.8087 (mmm-85) cc_final: 0.7659 (mmm-85) REVERT: B 142 ARG cc_start: 0.8487 (tpp80) cc_final: 0.8193 (tpp-160) REVERT: A 132 LYS cc_start: 0.7729 (tppt) cc_final: 0.7456 (tptp) REVERT: A 161 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6254 (pm20) REVERT: A 165 GLN cc_start: 0.7923 (mp10) cc_final: 0.7396 (mp10) REVERT: A 338 ARG cc_start: 0.7938 (mtp85) cc_final: 0.7619 (mtp85) REVERT: A 355 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6950 (tm-30) REVERT: A 447 GLU cc_start: 0.7328 (mp0) cc_final: 0.7051 (mp0) REVERT: A 526 LYS cc_start: 0.8377 (tppp) cc_final: 0.7953 (tppp) REVERT: A 542 MET cc_start: 0.7622 (tpp) cc_final: 0.7188 (tpp) REVERT: A 558 GLU cc_start: 0.7634 (pm20) cc_final: 0.7322 (pm20) REVERT: A 593 ASP cc_start: 0.7236 (t0) cc_final: 0.6801 (t0) REVERT: A 605 SER cc_start: 0.8044 (t) cc_final: 0.7717 (p) REVERT: A 663 LYS cc_start: 0.8011 (ptmm) cc_final: 0.7624 (ttpp) REVERT: A 667 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7360 (pm20) REVERT: A 692 MET cc_start: 0.6702 (mmm) cc_final: 0.6253 (mmm) REVERT: A 693 MET cc_start: 0.6951 (mtt) cc_final: 0.6656 (mtt) REVERT: A 743 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7672 (mm-30) REVERT: A 770 LEU cc_start: 0.8271 (tp) cc_final: 0.8061 (tt) REVERT: A 771 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: A 772 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7566 (mp0) REVERT: A 777 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7422 (m-30) REVERT: A 783 ASP cc_start: 0.7587 (m-30) cc_final: 0.7347 (m-30) REVERT: A 855 LYS cc_start: 0.8170 (tttt) cc_final: 0.7936 (tttt) outliers start: 59 outliers final: 22 residues processed: 386 average time/residue: 1.5476 time to fit residues: 641.5165 Evaluate side-chains 374 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 345 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 GLN 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 298 SER Chi-restraints excluded: chain C residue 355 GLU 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 605 SER Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain A residue 137 LEU 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 313 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 570 VAL Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 764 ASN Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 777 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 66 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.3980 chunk 88 optimal weight: 0.5980 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN C 354 ASN C 517 GLN C 626 ASN B 43 GLN B 112 ASN A 382 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 = 0.3879 r_free = 0.3879 target = 0.146687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124964 restraints weight = 18049.807| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.78 r_work: 0.3468 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2258 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= 0.139 Angle : 0.491 6.683 18856 Z= 0.250 Chirality : 0.039 0.124 2060 Planarity : 0.003 0.034 2442 Dihedral : 3.746 15.671 1846 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.05 % Allowed : 24.35 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.21), residues: 1648 helix: 1.14 (0.17), residues: 890 sheet: -1.42 (0.57), residues: 72 loop : 0.66 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 791 HIS 0.002 0.001 HIS D 31 PHE 0.010 0.001 PHE A 730 TYR 0.015 0.001 TYR B 77 ARG 0.004 0.000 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 656) hydrogen bonds : angle 4.60911 ( 1848) metal coordination : bond 0.00373 ( 16) metal coordination : angle 2.72809 ( 24) covalent geometry : bond 0.00323 (13948) covalent geometry : angle 0.48204 (18832) *********************** 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 430 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 368 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 132 LYS cc_start: 0.7791 (tppt) cc_final: 0.7576 (tppp) REVERT: C 137 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8197 (tp) REVERT: C 311 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8430 (mttp) REVERT: C 323 LYS cc_start: 0.8373 (mtpm) cc_final: 0.8167 (mtpp) REVERT: C 327 LEU cc_start: 0.8533 (tt) cc_final: 0.8303 (mt) REVERT: C 355 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: C 447 GLU cc_start: 0.7097 (pp20) cc_final: 0.6847 (pm20) REVERT: C 593 ASP cc_start: 0.7303 (t0) cc_final: 0.7003 (t0) REVERT: C 611 GLN cc_start: 0.8291 (mp10) cc_final: 0.7897 (mt0) REVERT: C 692 MET cc_start: 0.6855 (mmm) cc_final: 0.6446 (mmm) REVERT: C 693 MET cc_start: 0.7117 (mtt) cc_final: 0.6782 (mtt) REVERT: C 783 ASP cc_start: 0.7471 (m-30) cc_final: 0.7241 (m-30) REVERT: C 825 MET cc_start: 0.8662 (ttm) cc_final: 0.8371 (ttt) REVERT: C 829 LYS cc_start: 0.8805 (tttm) cc_final: 0.8590 (ttmt) REVERT: B 17 ARG cc_start: 0.7441 (ptm-80) cc_final: 0.7053 (ptm-80) REVERT: B 130 GLN cc_start: 0.8233 (mt0) cc_final: 0.7960 (mt0) REVERT: B 131 ARG cc_start: 0.8668 (mtm-85) cc_final: 0.8074 (mtt-85) REVERT: B 136 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7543 (mmm-85) REVERT: A 132 LYS cc_start: 0.7783 (tppt) cc_final: 0.7500 (tptp) REVERT: A 137 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8246 (tt) REVERT: A 165 GLN cc_start: 0.7924 (mp10) cc_final: 0.7407 (mp10) REVERT: A 338 ARG cc_start: 0.7888 (mtp85) cc_final: 0.7656 (mtp85) REVERT: A 339 MET cc_start: 0.8486 (mtp) cc_final: 0.8286 (mtt) REVERT: A 355 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6919 (tm-30) REVERT: A 447 GLU cc_start: 0.7385 (mp0) cc_final: 0.7072 (mp0) REVERT: A 526 LYS cc_start: 0.8372 (tppp) cc_final: 0.7947 (tppp) REVERT: A 558 GLU cc_start: 0.7482 (pm20) cc_final: 0.7237 (pm20) REVERT: A 605 SER cc_start: 0.7992 (t) cc_final: 0.7709 (p) REVERT: A 663 LYS cc_start: 0.7972 (ptmm) cc_final: 0.7686 (ttpp) REVERT: A 667 GLU cc_start: 0.7760 (pm20) cc_final: 0.7387 (pm20) REVERT: A 692 MET cc_start: 0.6785 (mmm) cc_final: 0.6343 (mmm) REVERT: A 693 MET cc_start: 0.7019 (mtt) cc_final: 0.6682 (mtt) REVERT: A 743 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7650 (mm-30) REVERT: A 770 LEU cc_start: 0.8204 (tp) cc_final: 0.7996 (tt) REVERT: A 777 ASP cc_start: 0.7630 (m-30) cc_final: 0.7426 (m-30) REVERT: A 782 ARG cc_start: 0.7380 (ttm-80) cc_final: 0.7137 (ttm-80) REVERT: A 855 LYS cc_start: 0.8091 (tttt) cc_final: 0.7888 (tttt) outliers start: 62 outliers final: 27 residues processed: 388 average time/residue: 1.5226 time to fit residues: 634.9031 Evaluate side-chains 385 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 353 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 137 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 292 GLU 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 537 LEU Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 137 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 355 GLU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 747 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 155 optimal weight: 0.4980 chunk 115 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 143 optimal weight: 0.1980 chunk 163 optimal weight: 0.0970 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 122 optimal weight: 0.0370 overall best weight: 0.2856 ------------------------------------------------------------------------------- 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 B 43 GLN B 112 ASN A 266 ASN A 626 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.146373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.125491 restraints weight = 18203.520| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.74 r_work: 0.3489 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13964 Z= 0.096 Angle : 0.460 7.916 18856 Z= 0.234 Chirality : 0.038 0.169 2060 Planarity : 0.003 0.032 2442 Dihedral : 3.590 14.903 1846 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.33 % Allowed : 24.35 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.21), residues: 1648 helix: 1.43 (0.18), residues: 876 sheet: -1.48 (0.57), residues: 72 loop : 0.75 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 791 HIS 0.002 0.000 HIS A 531 PHE 0.010 0.001 PHE C 733 TYR 0.011 0.001 TYR D 77 ARG 0.004 0.000 ARG C 735 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 656) hydrogen bonds : angle 4.38460 ( 1848) metal coordination : bond 0.00263 ( 16) metal coordination : angle 2.35246 ( 24) covalent geometry : bond 0.00219 (13948) covalent geometry : angle 0.45301 (18832) *********************** 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 408 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 357 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 24 THR cc_start: 0.8021 (m) cc_final: 0.7804 (m) REVERT: D 131 ARG cc_start: 0.8652 (mtm-85) cc_final: 0.8057 (mtt180) REVERT: C 132 LYS cc_start: 0.7797 (tppt) cc_final: 0.7564 (tppp) REVERT: C 137 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8201 (tp) REVERT: C 264 SER cc_start: 0.7938 (m) cc_final: 0.7699 (t) REVERT: C 270 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7422 (t0) REVERT: C 327 LEU cc_start: 0.8489 (tt) cc_final: 0.8274 (mt) REVERT: C 355 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: C 447 GLU cc_start: 0.7068 (pp20) cc_final: 0.6826 (pm20) REVERT: C 558 GLU cc_start: 0.7582 (pm20) cc_final: 0.7334 (pm20) REVERT: C 593 ASP cc_start: 0.7238 (t0) cc_final: 0.6989 (t0) REVERT: C 611 GLN cc_start: 0.8263 (mp10) cc_final: 0.7881 (mt0) REVERT: C 692 MET cc_start: 0.6837 (mmm) cc_final: 0.6429 (mmm) REVERT: C 693 MET cc_start: 0.7046 (mtt) cc_final: 0.6837 (mtt) REVERT: C 825 MET cc_start: 0.8607 (ttm) cc_final: 0.8356 (ttt) REVERT: B 17 ARG cc_start: 0.7430 (ptm-80) cc_final: 0.7020 (ptm-80) REVERT: B 130 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: B 131 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8195 (mtm-85) REVERT: A 132 LYS cc_start: 0.7818 (tppt) cc_final: 0.7503 (tptp) REVERT: A 137 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8246 (tt) REVERT: A 165 GLN cc_start: 0.7901 (mp10) cc_final: 0.7375 (mp10) REVERT: A 323 LYS cc_start: 0.8230 (mtpm) cc_final: 0.8023 (ttpp) REVERT: A 338 ARG cc_start: 0.7849 (mtp85) cc_final: 0.7570 (mtp85) REVERT: A 355 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6835 (tm-30) REVERT: A 447 GLU cc_start: 0.7373 (mp0) cc_final: 0.7056 (mp0) REVERT: A 522 TYR cc_start: 0.8537 (m-80) cc_final: 0.8257 (m-80) REVERT: A 526 LYS cc_start: 0.8345 (tppp) cc_final: 0.7860 (tppp) REVERT: A 558 GLU cc_start: 0.7467 (pm20) cc_final: 0.7220 (pm20) REVERT: A 605 SER cc_start: 0.7996 (t) cc_final: 0.7737 (p) REVERT: A 663 LYS cc_start: 0.7984 (ptmm) cc_final: 0.7634 (ttpp) REVERT: A 667 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: A 692 MET cc_start: 0.6799 (mmm) cc_final: 0.6295 (mmm) REVERT: A 693 MET cc_start: 0.6986 (mtt) cc_final: 0.6731 (mtt) REVERT: A 770 LEU cc_start: 0.8141 (tp) cc_final: 0.7939 (tt) REVERT: A 777 ASP cc_start: 0.7616 (m-30) cc_final: 0.7414 (m-30) REVERT: A 855 LYS cc_start: 0.8144 (tttt) cc_final: 0.7937 (tttt) outliers start: 51 outliers final: 18 residues processed: 371 average time/residue: 1.6259 time to fit residues: 648.1227 Evaluate side-chains 368 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 344 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 137 LEU 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 270 ASP 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 605 SER Chi-restraints excluded: chain C residue 667 GLU 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 137 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 665 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 716 LEU 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 0 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 A 266 ASN 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 = 0.3877 r_free = 0.3877 target = 0.146545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.124774 restraints weight = 17924.511| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.76 r_work: 0.3453 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13964 Z= 0.172 Angle : 0.514 7.921 18856 Z= 0.259 Chirality : 0.040 0.147 2060 Planarity : 0.003 0.031 2442 Dihedral : 3.780 16.010 1846 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.72 % Allowed : 24.09 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.21), residues: 1648 helix: 1.30 (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 TRP 0.007 0.001 TRP B 139 HIS 0.003 0.001 HIS B 85 PHE 0.013 0.002 PHE B 76 TYR 0.017 0.001 TYR B 77 ARG 0.004 0.000 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 656) hydrogen bonds : angle 4.51589 ( 1848) metal coordination : bond 0.00563 ( 16) metal coordination : angle 2.71973 ( 24) covalent geometry : bond 0.00407 (13948) covalent geometry : angle 0.50556 (18832) *********************** 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 425 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 368 time to evaluate : 1.752 Fit side-chains revert: symmetry clash REVERT: C 132 LYS cc_start: 0.7843 (tppt) cc_final: 0.7594 (tppp) REVERT: C 137 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8222 (tp) REVERT: C 268 GLU cc_start: 0.7127 (tt0) cc_final: 0.6917 (tt0) REVERT: C 338 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7788 (ttm-80) REVERT: C 355 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: C 593 ASP cc_start: 0.7285 (t0) cc_final: 0.7062 (t0) REVERT: C 611 GLN cc_start: 0.8326 (mp10) cc_final: 0.8119 (mp10) REVERT: C 692 MET cc_start: 0.6888 (mmm) cc_final: 0.6473 (mmm) REVERT: C 693 MET cc_start: 0.7092 (mtt) cc_final: 0.6841 (mtt) REVERT: B 17 ARG cc_start: 0.7477 (ptm-80) cc_final: 0.7060 (ptm-80) REVERT: B 130 GLN cc_start: 0.8230 (mt0) cc_final: 0.7998 (mt0) REVERT: B 131 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8190 (mtm-85) REVERT: A 128 LEU cc_start: 0.8335 (mp) cc_final: 0.8100 (mm) REVERT: A 132 LYS cc_start: 0.7852 (tppt) cc_final: 0.7518 (tptp) REVERT: A 137 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8259 (tt) REVERT: A 165 GLN cc_start: 0.7939 (mp10) cc_final: 0.7296 (mp-120) REVERT: A 323 LYS cc_start: 0.8282 (mtpm) cc_final: 0.8009 (mtpp) REVERT: A 338 ARG cc_start: 0.7816 (mtp85) cc_final: 0.7511 (mtp85) REVERT: A 339 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8237 (mtm) REVERT: A 355 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: A 435 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7440 (mtpt) REVERT: A 447 GLU cc_start: 0.7416 (mp0) cc_final: 0.7084 (mp0) REVERT: A 526 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8029 (ttpp) REVERT: A 605 SER cc_start: 0.8017 (t) cc_final: 0.7771 (p) REVERT: A 663 LYS cc_start: 0.7994 (ptmm) cc_final: 0.7667 (ttpp) REVERT: A 667 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7384 (pm20) REVERT: A 692 MET cc_start: 0.6888 (mmm) cc_final: 0.6377 (mmm) REVERT: A 693 MET cc_start: 0.7103 (mtt) cc_final: 0.6847 (mtt) REVERT: A 770 LEU cc_start: 0.8249 (tp) cc_final: 0.8044 (tt) outliers start: 57 outliers final: 25 residues processed: 383 average time/residue: 1.5740 time to fit residues: 647.4502 Evaluate side-chains 393 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 360 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain C residue 137 LEU 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 313 MET 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 534 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain A residue 137 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 339 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 159 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 0.0970 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 275 ASN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C 626 ASN A 626 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.146987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.125329 restraints weight = 18080.133| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.77 r_work: 0.3467 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13964 Z= 0.136 Angle : 0.504 8.759 18856 Z= 0.252 Chirality : 0.039 0.182 2060 Planarity : 0.003 0.034 2442 Dihedral : 3.716 15.589 1846 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.20 % Allowed : 24.80 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.21), residues: 1648 helix: 1.32 (0.18), residues: 900 sheet: -1.42 (0.58), residues: 72 loop : 0.64 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 139 HIS 0.002 0.001 HIS A 531 PHE 0.011 0.001 PHE B 76 TYR 0.015 0.001 TYR D 77 ARG 0.003 0.000 ARG C 338 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 656) hydrogen bonds : angle 4.42980 ( 1848) metal coordination : bond 0.00438 ( 16) metal coordination : angle 2.49881 ( 24) covalent geometry : bond 0.00321 (13948) covalent geometry : angle 0.49614 (18832) *********************** 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 417 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 368 time to evaluate : 1.696 Fit side-chains revert: symmetry clash REVERT: C 132 LYS cc_start: 0.7844 (tppt) cc_final: 0.7580 (tppp) REVERT: C 137 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8228 (tp) REVERT: C 264 SER cc_start: 0.7994 (m) cc_final: 0.7752 (t) REVERT: C 268 GLU cc_start: 0.7185 (tt0) cc_final: 0.6967 (tt0) REVERT: C 355 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: C 447 GLU cc_start: 0.7083 (pp20) cc_final: 0.6881 (pm20) REVERT: C 593 ASP cc_start: 0.7269 (t0) cc_final: 0.7038 (t0) REVERT: C 611 GLN cc_start: 0.8311 (mp10) cc_final: 0.7926 (mt0) REVERT: C 676 MET cc_start: 0.6952 (mpt) cc_final: 0.6707 (mpt) REVERT: C 692 MET cc_start: 0.6956 (mmm) cc_final: 0.6558 (mmm) REVERT: C 693 MET cc_start: 0.7037 (mtt) cc_final: 0.6812 (mtt) REVERT: B 17 ARG cc_start: 0.7471 (ptm-80) cc_final: 0.7067 (ptm-80) REVERT: B 131 ARG cc_start: 0.8681 (mtm-85) cc_final: 0.8198 (mtm-85) REVERT: A 128 LEU cc_start: 0.8360 (mp) cc_final: 0.8142 (mm) REVERT: A 132 LYS cc_start: 0.7875 (tppt) cc_final: 0.7535 (tptp) REVERT: A 137 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8267 (tt) REVERT: A 165 GLN cc_start: 0.7927 (mp10) cc_final: 0.7302 (mp-120) REVERT: A 323 LYS cc_start: 0.8244 (mtpm) cc_final: 0.7975 (mtpp) REVERT: A 338 ARG cc_start: 0.7790 (mtp85) cc_final: 0.7484 (mtp85) REVERT: A 339 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8162 (mtm) REVERT: A 341 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7812 (mt-10) REVERT: A 355 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6808 (tm-30) REVERT: A 435 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7478 (mtpt) REVERT: A 447 GLU cc_start: 0.7401 (mp0) cc_final: 0.7026 (mp0) REVERT: A 526 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7903 (ttpp) REVERT: A 605 SER cc_start: 0.8046 (t) cc_final: 0.7806 (p) REVERT: A 663 LYS cc_start: 0.8014 (ptmm) cc_final: 0.7645 (ttpp) REVERT: A 667 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7380 (pm20) REVERT: A 692 MET cc_start: 0.6908 (mmm) cc_final: 0.6394 (mmm) REVERT: A 693 MET cc_start: 0.7134 (mtt) cc_final: 0.6870 (mtt) REVERT: A 770 LEU cc_start: 0.8240 (tp) cc_final: 0.8038 (tt) outliers start: 49 outliers final: 28 residues processed: 382 average time/residue: 1.5684 time to fit residues: 642.9268 Evaluate side-chains 387 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 351 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 137 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 292 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 318 LEU 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 665 LEU Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain A residue 137 LEU 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 339 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 665 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 739 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 115 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 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 A 626 ASN A 841 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.146293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124404 restraints weight = 18018.828| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.78 r_work: 0.3455 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13964 Z= 0.160 Angle : 0.525 8.404 18856 Z= 0.264 Chirality : 0.040 0.177 2060 Planarity : 0.003 0.034 2442 Dihedral : 3.804 15.718 1846 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.46 % Allowed : 24.74 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.21), residues: 1648 helix: 1.31 (0.18), residues: 890 sheet: -1.43 (0.58), residues: 72 loop : 0.61 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 139 HIS 0.003 0.001 HIS C 297 PHE 0.012 0.001 PHE B 76 TYR 0.016 0.001 TYR D 77 ARG 0.004 0.000 ARG A 539 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 656) hydrogen bonds : angle 4.47258 ( 1848) metal coordination : bond 0.00498 ( 16) metal coordination : angle 2.60890 ( 24) covalent geometry : bond 0.00380 (13948) covalent geometry : angle 0.51669 (18832) *********************** 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 422 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 369 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 129 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7685 (p) REVERT: C 132 LYS cc_start: 0.7854 (tppt) cc_final: 0.7640 (tppp) REVERT: C 137 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8211 (tp) REVERT: C 264 SER cc_start: 0.8007 (m) cc_final: 0.7756 (t) REVERT: C 355 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: C 447 GLU cc_start: 0.7297 (pp20) cc_final: 0.7070 (pm20) REVERT: C 593 ASP cc_start: 0.7287 (t0) cc_final: 0.7054 (t0) REVERT: C 611 GLN cc_start: 0.8341 (mp10) cc_final: 0.7920 (mt0) REVERT: C 676 MET cc_start: 0.6956 (mpt) cc_final: 0.6695 (mpt) REVERT: C 692 MET cc_start: 0.6907 (mmm) cc_final: 0.6515 (mmm) REVERT: C 693 MET cc_start: 0.7083 (mtt) cc_final: 0.6836 (mtt) REVERT: B 17 ARG cc_start: 0.7493 (ptm-80) cc_final: 0.7094 (ptm-80) REVERT: B 131 ARG cc_start: 0.8691 (mtm-85) cc_final: 0.8188 (mtm-85) REVERT: A 128 LEU cc_start: 0.8412 (mp) cc_final: 0.8201 (mm) REVERT: A 132 LYS cc_start: 0.7883 (tppt) cc_final: 0.7537 (tptp) REVERT: A 165 GLN cc_start: 0.7940 (mp10) cc_final: 0.7411 (mp-120) REVERT: A 323 LYS cc_start: 0.8262 (mtpm) cc_final: 0.7997 (mtpp) REVERT: A 338 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7495 (mtp85) REVERT: A 339 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8167 (mtm) REVERT: A 341 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 355 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6844 (tm-30) REVERT: A 435 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7474 (mtpt) REVERT: A 447 GLU cc_start: 0.7383 (mp0) cc_final: 0.7000 (mp0) REVERT: A 605 SER cc_start: 0.8053 (t) cc_final: 0.7799 (p) REVERT: A 663 LYS cc_start: 0.8010 (ptmm) cc_final: 0.7698 (ttpp) REVERT: A 667 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7380 (pm20) REVERT: A 692 MET cc_start: 0.6948 (mmm) cc_final: 0.6459 (mmm) REVERT: A 693 MET cc_start: 0.7226 (mtt) cc_final: 0.6929 (mtt) REVERT: A 763 ARG cc_start: 0.7508 (mtp85) cc_final: 0.7263 (ttp80) outliers start: 53 outliers final: 31 residues processed: 388 average time/residue: 1.5104 time to fit residues: 629.2736 Evaluate side-chains 394 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 356 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 137 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 318 LEU 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 491 LEU 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 665 LEU Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain A residue 129 THR 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 318 LEU Chi-restraints excluded: chain A residue 339 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 537 LEU 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 739 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 3 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 117 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 overall best weight: 0.6440 ------------------------------------------------------------------------------- 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 344 GLN C 517 GLN C 626 ASN ** 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 = 0.3877 r_free = 0.3877 target = 0.146617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125047 restraints weight = 17958.796| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.76 r_work: 0.3464 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13964 Z= 0.142 Angle : 0.528 9.300 18856 Z= 0.265 Chirality : 0.040 0.166 2060 Planarity : 0.003 0.036 2442 Dihedral : 3.799 18.404 1846 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.55 % Allowed : 26.04 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.21), residues: 1648 helix: 1.35 (0.18), residues: 890 sheet: -1.54 (0.59), residues: 72 loop : 0.61 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 139 HIS 0.003 0.001 HIS C 841 PHE 0.011 0.001 PHE B 76 TYR 0.015 0.001 TYR D 77 ARG 0.004 0.000 ARG A 539 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 656) hydrogen bonds : angle 4.42763 ( 1848) metal coordination : bond 0.00477 ( 16) metal coordination : angle 2.53178 ( 24) covalent geometry : bond 0.00337 (13948) covalent geometry : angle 0.52087 (18832) *********************** 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 403 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 364 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 129 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7665 (p) REVERT: C 132 LYS cc_start: 0.7878 (tppt) cc_final: 0.7676 (tppp) REVERT: C 137 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8214 (tp) REVERT: C 264 SER cc_start: 0.7990 (m) cc_final: 0.7745 (t) REVERT: C 268 GLU cc_start: 0.7210 (tt0) cc_final: 0.6996 (tt0) REVERT: C 355 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: C 447 GLU cc_start: 0.7321 (pp20) cc_final: 0.7058 (pm20) REVERT: C 593 ASP cc_start: 0.7242 (t0) cc_final: 0.7033 (t0) REVERT: C 611 GLN cc_start: 0.8310 (mp10) cc_final: 0.7946 (mt0) REVERT: C 676 MET cc_start: 0.6980 (mpt) cc_final: 0.6689 (mpt) REVERT: C 692 MET cc_start: 0.6885 (mmm) cc_final: 0.6515 (mmm) REVERT: C 693 MET cc_start: 0.7039 (mtt) cc_final: 0.6790 (mtt) REVERT: B 17 ARG cc_start: 0.7464 (ptm-80) cc_final: 0.7087 (ptm-80) REVERT: B 131 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8197 (mtm-85) REVERT: B 142 ARG cc_start: 0.8585 (tpp-160) cc_final: 0.8297 (ttm110) REVERT: A 128 LEU cc_start: 0.8405 (mp) cc_final: 0.8187 (mm) REVERT: A 132 LYS cc_start: 0.7889 (tppt) cc_final: 0.7544 (tptp) REVERT: A 165 GLN cc_start: 0.7961 (mp10) cc_final: 0.7731 (mp-120) REVERT: A 323 LYS cc_start: 0.8262 (mtpm) cc_final: 0.8008 (mtpp) REVERT: A 338 ARG cc_start: 0.7768 (mtp85) cc_final: 0.7451 (mtp85) REVERT: A 341 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7791 (mt-10) REVERT: A 355 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6834 (tm-30) REVERT: A 435 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7479 (mtpt) REVERT: A 447 GLU cc_start: 0.7494 (mp0) cc_final: 0.7114 (mp0) REVERT: A 605 SER cc_start: 0.8042 (t) cc_final: 0.7816 (p) REVERT: A 663 LYS cc_start: 0.8005 (ptmm) cc_final: 0.7706 (ttpp) REVERT: A 667 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: A 692 MET cc_start: 0.6910 (mmm) cc_final: 0.6442 (mmm) REVERT: A 693 MET cc_start: 0.7222 (mtt) cc_final: 0.6931 (mtt) outliers start: 39 outliers final: 29 residues processed: 376 average time/residue: 1.5791 time to fit residues: 638.1931 Evaluate side-chains 386 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 351 time to evaluate : 1.713 ------------------------------------------------------------------------------- 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 129 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 318 LEU 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 534 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain A residue 129 THR 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 537 LEU 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 739 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 35 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 117 optimal weight: 0.0470 chunk 42 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 344 GLN C 345 GLN C 517 GLN C 626 ASN ** 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 = 0.3859 r_free = 0.3859 target = 0.145133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.124126 restraints weight = 18210.557| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.73 r_work: 0.3462 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13964 Z= 0.150 Angle : 0.544 10.155 18856 Z= 0.272 Chirality : 0.040 0.160 2060 Planarity : 0.003 0.037 2442 Dihedral : 3.828 19.718 1846 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.48 % Allowed : 26.31 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.21), residues: 1648 helix: 1.32 (0.18), residues: 890 sheet: -1.62 (0.58), residues: 72 loop : 0.59 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 139 HIS 0.003 0.001 HIS C 841 PHE 0.011 0.001 PHE B 76 TYR 0.016 0.001 TYR D 77 ARG 0.005 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 656) hydrogen bonds : angle 4.44617 ( 1848) metal coordination : bond 0.00497 ( 16) metal coordination : angle 2.60359 ( 24) covalent geometry : bond 0.00358 (13948) covalent geometry : angle 0.53589 (18832) *********************** 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 399 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 361 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 129 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7676 (p) REVERT: C 132 LYS cc_start: 0.7883 (tppt) cc_final: 0.7682 (tppp) REVERT: C 137 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8192 (tp) REVERT: C 264 SER cc_start: 0.7993 (m) cc_final: 0.7735 (t) REVERT: C 268 GLU cc_start: 0.7201 (tt0) cc_final: 0.6945 (tp30) REVERT: C 355 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: C 447 GLU cc_start: 0.7324 (pp20) cc_final: 0.7073 (pm20) REVERT: C 593 ASP cc_start: 0.7246 (t0) cc_final: 0.7024 (t0) REVERT: C 597 LYS cc_start: 0.8471 (mttm) cc_final: 0.8242 (mtpp) REVERT: C 611 GLN cc_start: 0.8310 (mp10) cc_final: 0.7953 (mt0) REVERT: C 692 MET cc_start: 0.6885 (mmm) cc_final: 0.6515 (mmm) REVERT: C 693 MET cc_start: 0.7038 (mtt) cc_final: 0.6789 (mtt) REVERT: B 17 ARG cc_start: 0.7463 (ptm-80) cc_final: 0.7092 (ptm-80) REVERT: B 131 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8194 (mtm-85) REVERT: A 128 LEU cc_start: 0.8374 (mp) cc_final: 0.8162 (mm) REVERT: A 132 LYS cc_start: 0.7908 (tppt) cc_final: 0.7561 (tptp) REVERT: A 165 GLN cc_start: 0.7925 (mp10) cc_final: 0.7660 (mp-120) REVERT: A 323 LYS cc_start: 0.8258 (mtpm) cc_final: 0.8008 (mtpp) REVERT: A 338 ARG cc_start: 0.7770 (mtp85) cc_final: 0.7453 (mtp85) REVERT: A 341 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7795 (mt-10) REVERT: A 355 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: A 435 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7472 (mtpt) REVERT: A 447 GLU cc_start: 0.7362 (mp0) cc_final: 0.6984 (mp0) REVERT: A 605 SER cc_start: 0.8058 (t) cc_final: 0.7828 (p) REVERT: A 663 LYS cc_start: 0.7989 (ptmm) cc_final: 0.7747 (ttpp) REVERT: A 667 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7337 (pm20) REVERT: A 692 MET cc_start: 0.6916 (mmm) cc_final: 0.6444 (mmm) REVERT: A 693 MET cc_start: 0.7232 (mtt) cc_final: 0.6942 (mtt) outliers start: 38 outliers final: 28 residues processed: 375 average time/residue: 1.8049 time to fit residues: 727.0359 Evaluate side-chains 391 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 357 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 129 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 462 LYS 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 587 ILE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 144 MET 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 318 LEU 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 537 LEU 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 739 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 108 optimal weight: 0.0370 chunk 26 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 78 optimal weight: 0.2980 chunk 133 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 C 517 GLN C 626 ASN ** 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 = 0.3893 r_free = 0.3893 target = 0.147858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.126441 restraints weight = 17855.531| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.76 r_work: 0.3475 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13964 Z= 0.120 Angle : 0.529 11.377 18856 Z= 0.263 Chirality : 0.039 0.145 2060 Planarity : 0.003 0.038 2442 Dihedral : 3.737 16.427 1846 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.89 % Allowed : 27.09 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.21), residues: 1648 helix: 1.43 (0.18), residues: 890 sheet: -1.60 (0.58), residues: 72 loop : 0.61 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 139 HIS 0.003 0.001 HIS C 841 PHE 0.011 0.001 PHE B 76 TYR 0.013 0.001 TYR D 77 ARG 0.005 0.000 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 656) hydrogen bonds : angle 4.37058 ( 1848) metal coordination : bond 0.00349 ( 16) metal coordination : angle 2.71157 ( 24) covalent geometry : bond 0.00282 (13948) covalent geometry : angle 0.52057 (18832) ********************** 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 385 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 356 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 131 ARG cc_start: 0.8672 (mtm-85) cc_final: 0.8276 (mtt180) REVERT: C 129 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7611 (p) REVERT: C 132 LYS cc_start: 0.7869 (tppt) cc_final: 0.7667 (tppp) REVERT: C 264 SER cc_start: 0.7936 (m) cc_final: 0.7682 (t) REVERT: C 268 GLU cc_start: 0.7195 (tt0) cc_final: 0.6919 (tm-30) REVERT: C 355 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: C 447 GLU cc_start: 0.7303 (pp20) cc_final: 0.7042 (pm20) REVERT: C 502 TYR cc_start: 0.8232 (m-80) cc_final: 0.7978 (m-80) REVERT: C 593 ASP cc_start: 0.7205 (t0) cc_final: 0.6993 (t0) REVERT: C 597 LYS cc_start: 0.8459 (mttm) cc_final: 0.8228 (mtpp) REVERT: C 611 GLN cc_start: 0.8297 (mp10) cc_final: 0.7953 (mt0) REVERT: C 692 MET cc_start: 0.6903 (mmm) cc_final: 0.6545 (mmm) REVERT: C 771 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: B 17 ARG cc_start: 0.7458 (ptm-80) cc_final: 0.7087 (ptm-80) REVERT: B 131 ARG cc_start: 0.8678 (mtm-85) cc_final: 0.8200 (mtm-85) REVERT: A 128 LEU cc_start: 0.8335 (mp) cc_final: 0.8133 (mm) REVERT: A 132 LYS cc_start: 0.7914 (tppt) cc_final: 0.7592 (tptp) REVERT: A 137 LEU cc_start: 0.8424 (tp) cc_final: 0.8206 (tt) REVERT: A 165 GLN cc_start: 0.7944 (mp10) cc_final: 0.7703 (mp-120) REVERT: A 323 LYS cc_start: 0.8253 (mtpm) cc_final: 0.8000 (mtpp) REVERT: A 338 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7430 (mtp85) REVERT: A 341 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7795 (mt-10) REVERT: A 355 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6821 (tm-30) REVERT: A 447 GLU cc_start: 0.7415 (mp0) cc_final: 0.7031 (mp0) REVERT: A 605 SER cc_start: 0.8062 (t) cc_final: 0.7839 (p) REVERT: A 663 LYS cc_start: 0.7976 (ptmm) cc_final: 0.7691 (ttpp) REVERT: A 667 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7337 (pm20) REVERT: A 692 MET cc_start: 0.6974 (mmm) cc_final: 0.6549 (mmm) REVERT: A 693 MET cc_start: 0.7190 (mtt) cc_final: 0.6883 (mtt) outliers start: 29 outliers final: 21 residues processed: 367 average time/residue: 1.7649 time to fit residues: 695.9522 Evaluate side-chains 377 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 352 time to evaluate : 2.423 ------------------------------------------------------------------------------- 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 129 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 771 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 144 MET 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 318 LEU Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 667 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 58 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 19 optimal weight: 0.0670 chunk 136 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 143 optimal weight: 0.0670 chunk 130 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 GLN D 114 GLN C 345 GLN C 517 GLN C 626 ASN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN A 626 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 = 0.3891 r_free = 0.3891 target = 0.147726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126123 restraints weight = 18028.733| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.78 r_work: 0.3470 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13964 Z= 0.118 Angle : 0.543 11.095 18856 Z= 0.269 Chirality : 0.039 0.149 2060 Planarity : 0.003 0.037 2442 Dihedral : 3.744 17.221 1846 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.15 % Allowed : 27.02 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.21), residues: 1648 helix: 1.40 (0.18), residues: 902 sheet: -1.53 (0.59), residues: 72 loop : 0.61 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 139 HIS 0.002 0.001 HIS C 841 PHE 0.010 0.001 PHE C 733 TYR 0.015 0.001 TYR A 380 ARG 0.006 0.000 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 656) hydrogen bonds : angle 4.37026 ( 1848) metal coordination : bond 0.00328 ( 16) metal coordination : angle 2.59802 ( 24) covalent geometry : bond 0.00278 (13948) covalent geometry : angle 0.53520 (18832) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14487.50 seconds wall clock time: 251 minutes 44.36 seconds (15104.36 seconds total)