Starting phenix.real_space_refine on Sat Aug 23 17:48:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jro_36600/08_2025/8jro_36600.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jro_36600/08_2025/8jro_36600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jro_36600/08_2025/8jro_36600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jro_36600/08_2025/8jro_36600.map" model { file = "/net/cci-nas-00/data/ceres_data/8jro_36600/08_2025/8jro_36600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jro_36600/08_2025/8jro_36600.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13672 Number of models: 1 Model: "" Number of chains: 3 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: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 241 SG CYS D 37 80.979 76.140 92.664 1.00 49.18 S ATOM 266 SG CYS D 40 81.927 73.375 94.938 1.00 52.17 S ATOM 522 SG CYS D 70 83.216 73.440 91.258 1.00 54.24 S ATOM 545 SG CYS D 73 79.724 72.473 91.996 1.00 68.14 S ATOM 864 SG CYS D 110 81.395 73.463 74.747 1.00 60.52 S ATOM 886 SG CYS D 113 83.538 74.743 77.528 1.00 55.65 S ATOM 1148 SG CYS D 143 85.036 73.863 74.071 1.00 71.13 S ATOM 1168 SG CYS D 146 83.912 71.087 76.387 1.00 63.68 S Restraints were copied for chains: B, A Time building chain proxies: 4.95, per 1000 atoms: 0.36 Number of scatterers: 13672 At special positions: 0 Unit cell: (144.585, 110.313, 113.526, 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: 0.75 Conformation dependent library (CDL) restraints added in 530.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " 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 70 " 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 113 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 143 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 146 " pdb=" ZN D 201 " 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 70 " 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 113 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 143 " 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: 88 helices and 14 sheets defined 61.1% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'D' and resid 18 through 26 removed outlier: 3.779A pdb=" N THR D 24 " --> pdb=" O PRO D 20 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU D 25 " --> pdb=" O GLN D 21 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) 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 144 through 148 removed outlier: 3.928A pdb=" N ARG D 148 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 142 removed outlier: 4.049A pdb=" N ILE C 136 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.721A pdb=" N ILE C 150 " --> pdb=" O TYR C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 165 removed outlier: 3.879A pdb=" N GLN C 165 " --> pdb=" O GLU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 247 removed outlier: 3.505A pdb=" N THR C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 274 removed outlier: 3.543A pdb=" N THR C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Proline residue: C 265 - end of helix removed outlier: 3.563A pdb=" N TYR C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 removed outlier: 3.545A pdb=" N TYR C 283 " --> pdb=" O ASP C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 284 through 292 removed outlier: 3.561A pdb=" N ILE C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 289 " --> pdb=" O ASN C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 302 removed outlier: 3.759A pdb=" N LEU C 296 " --> pdb=" O ASN C 293 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS C 297 " --> pdb=" O ARG C 294 " (cutoff:3.500A) Proline residue: C 299 - end of helix removed outlier: 3.604A pdb=" N LEU C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 314 removed outlier: 3.669A pdb=" N LEU C 308 " --> pdb=" O MET C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 329 Processing helix chain 'C' and resid 332 through 354 removed outlier: 3.748A pdb=" N PHE C 343 " --> pdb=" O MET C 339 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN C 354 " --> pdb=" O LYS C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 386 removed outlier: 3.724A pdb=" N MET C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 378 " --> pdb=" O CYS C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 414 Processing helix chain 'C' and resid 426 through 433 removed outlier: 3.578A pdb=" N THR C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C 431 " --> pdb=" O PRO C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.626A 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: 3.744A 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 514 removed outlier: 3.545A pdb=" N GLU C 504 " --> pdb=" O ARG C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 547 removed outlier: 3.816A pdb=" N MET C 542 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET C 545 " --> pdb=" O GLU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 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 626 Processing helix chain 'C' and resid 634 through 642 removed outlier: 3.951A pdb=" N TYR C 638 " --> pdb=" O PRO C 634 " (cutoff:3.500A) removed outlier: 3.747A 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: 4.141A pdb=" N SER C 654 " --> pdb=" O ASP C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 668 removed outlier: 4.184A pdb=" N LEU C 665 " --> pdb=" O SER C 661 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 666 " --> pdb=" O LEU C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 723 removed outlier: 3.815A pdb=" N VAL C 714 " --> pdb=" O ARG C 710 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP C 719 " --> pdb=" O ASN C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 742 removed outlier: 4.087A pdb=" N VAL C 740 " --> pdb=" O GLY C 736 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 741 " --> pdb=" O PHE C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 750 Processing helix chain 'C' and resid 751 through 760 removed outlier: 4.066A pdb=" N GLU C 756 " --> pdb=" O PRO C 752 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C 757 " --> pdb=" O GLU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 773 Processing helix chain 'C' and resid 784 through 795 removed outlier: 3.730A pdb=" N GLU C 792 " --> pdb=" O ARG C 788 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 793 " --> pdb=" O GLU C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 810 Processing helix chain 'C' and resid 819 through 823 Processing helix chain 'C' and resid 854 through 869 removed outlier: 3.519A pdb=" N TYR C 868 " --> pdb=" O LYS C 864 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 869 " --> pdb=" O ALA C 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.779A pdb=" N THR B 24 " --> pdb=" O PRO B 20 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) 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 144 through 148 removed outlier: 3.928A pdb=" N ARG B 148 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 4.049A pdb=" N ILE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.721A pdb=" N ILE A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.879A pdb=" N GLN A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 removed outlier: 3.505A pdb=" N THR A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 274 removed outlier: 3.543A pdb=" N THR A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Proline residue: A 265 - end of helix removed outlier: 3.563A pdb=" N TYR A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.545A pdb=" N TYR A 283 " --> pdb=" O ASP A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.561A pdb=" N ILE A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.759A pdb=" N LEU A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Proline residue: A 299 - end of helix removed outlier: 3.604A pdb=" N LEU A 302 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 removed outlier: 3.669A pdb=" N LEU A 308 " --> pdb=" O MET A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 329 Processing helix chain 'A' and resid 332 through 354 removed outlier: 3.748A pdb=" N PHE A 343 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 386 removed outlier: 3.724A pdb=" N MET A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 378 " --> pdb=" O CYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 414 Processing helix chain 'A' and resid 426 through 433 removed outlier: 3.578A pdb=" N THR A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 431 " --> pdb=" O PRO A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.626A 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: 3.744A 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 514 removed outlier: 3.545A pdb=" N GLU A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 removed outlier: 3.816A pdb=" N MET A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 545 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 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 626 Processing helix chain 'A' and resid 634 through 642 removed outlier: 3.951A pdb=" N TYR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 3.747A 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: 4.141A pdb=" N SER A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 668 removed outlier: 4.184A pdb=" N LEU A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 723 removed outlier: 3.815A pdb=" N VAL A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 742 removed outlier: 4.087A pdb=" N VAL A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 741 " --> pdb=" O PHE A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 Processing helix chain 'A' and resid 751 through 760 removed outlier: 4.066A pdb=" N GLU A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 773 Processing helix chain 'A' and resid 784 through 795 removed outlier: 3.730A pdb=" N GLU A 792 " --> pdb=" O ARG A 788 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE A 793 " --> pdb=" O GLU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 810 Processing helix chain 'A' and resid 819 through 823 Processing helix chain 'A' and resid 854 through 869 removed outlier: 3.519A pdb=" N TYR A 868 " --> pdb=" O LYS A 864 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 869 " --> pdb=" O ALA A 865 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 36 through 37 removed outlier: 6.170A pdb=" N GLU D 36 " --> pdb=" O ALA D 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 86 through 90 removed outlier: 3.544A pdb=" N TYR D 88 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.756A 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: 6.583A 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 removed outlier: 3.717A pdb=" N LEU C 598 " --> pdb=" O ASP C 593 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 681 through 684 Processing sheet with id=AA7, first strand: chain 'C' and resid 775 through 777 removed outlier: 6.651A pdb=" N GLU C 775 " --> pdb=" O ILE C 827 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LYS C 829 " --> pdb=" O GLU C 775 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP C 777 " --> pdb=" O LYS C 829 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE C 826 " --> pdb=" O LEU C 847 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU C 849 " --> pdb=" O ILE C 826 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ALA C 828 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.170A pdb=" N GLU B 36 " --> pdb=" O ALA B 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 86 through 90 removed outlier: 3.544A pdb=" N TYR B 88 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.756A 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: 6.583A 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 removed outlier: 3.717A pdb=" N LEU A 598 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 681 through 684 Processing sheet with id=AB5, first strand: chain 'A' and resid 775 through 777 removed outlier: 6.651A pdb=" N GLU A 775 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LYS A 829 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP A 777 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 826 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 849 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ALA A 828 " --> pdb=" O LEU A 849 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1740 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: 1.86 Time building geometry restraints manager: 1.08 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: 4492 1.34 - 1.46: 3034 1.46 - 1.58: 6302 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 13948 Sorted by residual: bond pdb=" CB ASN C 275 " pdb=" CG ASN C 275 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.84e-01 bond pdb=" CB ASN A 275 " pdb=" CG ASN A 275 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.84e-01 bond pdb=" CB GLN B 27 " pdb=" CG GLN B 27 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.32e-01 bond pdb=" CB GLN D 27 " pdb=" CG GLN D 27 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.32e-01 bond pdb=" CG GLN B 27 " pdb=" CD GLN B 27 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 4.92e-01 ... (remaining 13943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 18500 1.50 - 3.01: 264 3.01 - 4.51: 52 4.51 - 6.01: 10 6.01 - 7.52: 6 Bond angle restraints: 18832 Sorted by residual: angle pdb=" N VAL C 740 " pdb=" CA VAL C 740 " pdb=" C VAL C 740 " ideal model delta sigma weight residual 113.53 110.06 3.47 9.80e-01 1.04e+00 1.25e+01 angle pdb=" N VAL A 740 " pdb=" CA VAL A 740 " pdb=" C VAL A 740 " ideal model delta sigma weight residual 113.53 110.06 3.47 9.80e-01 1.04e+00 1.25e+01 angle pdb=" N ILE D 30 " pdb=" CA ILE D 30 " pdb=" C ILE D 30 " ideal model delta sigma weight residual 113.07 108.70 4.37 1.36e+00 5.41e-01 1.03e+01 angle pdb=" N ILE B 30 " pdb=" CA ILE B 30 " pdb=" C ILE B 30 " ideal model delta sigma weight residual 113.07 108.70 4.37 1.36e+00 5.41e-01 1.03e+01 angle pdb=" CB MET C 304 " pdb=" CG MET C 304 " pdb=" SD MET C 304 " ideal model delta sigma weight residual 112.70 120.22 -7.52 3.00e+00 1.11e-01 6.28e+00 ... (remaining 18827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7314 17.94 - 35.88: 902 35.88 - 53.83: 260 53.83 - 71.77: 36 71.77 - 89.71: 16 Dihedral angle restraints: 8528 sinusoidal: 3612 harmonic: 4916 Sorted by residual: dihedral pdb=" CG ARG C 763 " pdb=" CD ARG C 763 " pdb=" NE ARG C 763 " pdb=" CZ ARG C 763 " ideal model delta sinusoidal sigma weight residual -90.00 -133.98 43.98 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG A 763 " pdb=" CD ARG A 763 " pdb=" NE ARG A 763 " pdb=" CZ ARG A 763 " ideal model delta sinusoidal sigma weight residual -90.00 -133.98 43.98 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CA ASP A 813 " pdb=" CB ASP A 813 " pdb=" CG ASP A 813 " pdb=" OD1 ASP A 813 " ideal model delta sinusoidal sigma weight residual -30.00 -84.76 54.76 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 8525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 978 0.024 - 0.048: 634 0.048 - 0.072: 308 0.072 - 0.096: 80 0.096 - 0.119: 60 Chirality restraints: 2060 Sorted by residual: chirality pdb=" CA ILE A 401 " pdb=" N ILE A 401 " pdb=" C ILE A 401 " pdb=" CB ILE A 401 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CA ILE C 401 " pdb=" N ILE C 401 " pdb=" C ILE C 401 " pdb=" CB ILE C 401 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CA PRO A 481 " pdb=" N PRO A 481 " pdb=" C PRO A 481 " pdb=" CB PRO A 481 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 2057 not shown) Planarity restraints: 2442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 306 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO C 307 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 306 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 307 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 744 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO A 745 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 745 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 745 " -0.017 5.00e-02 4.00e+02 ... (remaining 2439 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 500 2.72 - 3.26: 13760 3.26 - 3.81: 21308 3.81 - 4.35: 27938 4.35 - 4.90: 46188 Nonbonded interactions: 109694 Sorted by model distance: nonbonded pdb=" OH TYR B 86 " pdb=" OG SER B 89 " model vdw 2.174 3.040 nonbonded pdb=" OH TYR D 86 " pdb=" OG SER D 89 " model vdw 2.174 3.040 nonbonded pdb=" OE2 GLU A 303 " pdb=" OH TYR A 349 " model vdw 2.187 3.040 nonbonded pdb=" OE2 GLU C 303 " pdb=" OH TYR C 349 " model vdw 2.187 3.040 nonbonded pdb=" OG1 THR A 679 " pdb=" O GLY A 700 " model vdw 2.218 3.040 ... (remaining 109689 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: 0.03 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.140 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 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:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.003 0.038 13964 Z= 0.142 Angle : 0.514 7.518 18856 Z= 0.269 Chirality : 0.039 0.119 2060 Planarity : 0.003 0.032 2442 Dihedral : 16.679 89.709 5352 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.26 % Allowed : 20.37 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.20), residues: 1648 helix: -0.64 (0.17), residues: 866 sheet: -0.18 (0.60), residues: 92 loop : -0.21 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.015 0.001 TYR B 77 PHE 0.012 0.001 PHE A 475 TRP 0.005 0.001 TRP C 328 HIS 0.002 0.000 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00347 (13948) covalent geometry : angle 0.50192 (18832) hydrogen bonds : bond 0.25586 ( 624) hydrogen bonds : angle 7.65896 ( 1740) metal coordination : bond 0.00307 ( 16) metal coordination : angle 3.16739 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 389 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: D 112 ASN cc_start: 0.8667 (m110) cc_final: 0.8433 (m-40) REVERT: C 122 PHE cc_start: 0.7219 (m-80) cc_final: 0.6969 (m-10) REVERT: C 138 GLU cc_start: 0.6982 (tp30) cc_final: 0.6754 (tp30) REVERT: C 268 GLU cc_start: 0.7706 (tt0) cc_final: 0.7019 (tm-30) REVERT: C 301 TYR cc_start: 0.8471 (m-80) cc_final: 0.8256 (m-80) REVERT: C 457 VAL cc_start: 0.8725 (m) cc_final: 0.8187 (p) REVERT: C 459 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7061 (mm-30) REVERT: C 480 CYS cc_start: 0.7669 (p) cc_final: 0.7333 (p) REVERT: C 552 LYS cc_start: 0.8214 (mttp) cc_final: 0.7889 (mttm) REVERT: C 635 MET cc_start: 0.8226 (tpp) cc_final: 0.7979 (tpp) REVERT: C 642 MET cc_start: 0.8956 (mmm) cc_final: 0.8720 (mmm) REVERT: C 712 GLU cc_start: 0.7496 (tt0) cc_final: 0.7235 (tp30) REVERT: C 719 ASP cc_start: 0.8029 (t70) cc_final: 0.7672 (t0) REVERT: C 728 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7902 (mmmm) REVERT: C 766 ASP cc_start: 0.7696 (t0) cc_final: 0.7460 (t0) REVERT: C 793 ILE cc_start: 0.8451 (mt) cc_final: 0.8218 (mt) REVERT: C 822 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7873 (mmtm) REVERT: A 122 PHE cc_start: 0.7092 (m-80) cc_final: 0.6866 (m-10) REVERT: A 262 TYR cc_start: 0.6539 (t80) cc_final: 0.6250 (t80) REVERT: A 268 GLU cc_start: 0.7556 (tt0) cc_final: 0.6906 (tm-30) REVERT: A 387 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6646 (mt-10) REVERT: A 426 ASP cc_start: 0.7361 (t0) cc_final: 0.7006 (t0) REVERT: A 441 LYS cc_start: 0.8442 (tptp) cc_final: 0.8135 (tptp) REVERT: A 457 VAL cc_start: 0.8680 (m) cc_final: 0.8141 (p) REVERT: A 459 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7057 (mm-30) REVERT: A 480 CYS cc_start: 0.7718 (p) cc_final: 0.7443 (p) REVERT: A 525 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8517 (mt) REVERT: A 534 ASP cc_start: 0.7537 (m-30) cc_final: 0.7327 (m-30) REVERT: A 552 LYS cc_start: 0.8274 (mttp) cc_final: 0.7951 (mmtm) REVERT: A 635 MET cc_start: 0.8177 (tpp) cc_final: 0.7898 (tpp) REVERT: A 653 ASP cc_start: 0.7848 (m-30) cc_final: 0.7338 (p0) REVERT: A 667 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7412 (mt-10) REVERT: A 728 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7942 (mmmm) REVERT: A 766 ASP cc_start: 0.7593 (t0) cc_final: 0.7392 (t0) REVERT: A 793 ILE cc_start: 0.8526 (mt) cc_final: 0.8298 (mt) REVERT: A 825 MET cc_start: 0.8392 (ttt) cc_final: 0.8190 (ttt) outliers start: 4 outliers final: 2 residues processed: 389 average time/residue: 0.1398 time to fit residues: 73.5908 Evaluate side-chains 356 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 353 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 742 ASN Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 742 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 ASN C 321 GLN C 335 GLN C 357 ASN C 392 HIS C 451 ASN C 684 GLN C 715 ASN C 795 HIS C 845 ASN B 112 ASN A 321 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 392 HIS A 451 ASN A 681 GLN A 715 ASN A 795 HIS A 845 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111785 restraints weight = 19661.467| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.32 r_work: 0.3278 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 13964 Z= 0.272 Angle : 0.626 8.786 18856 Z= 0.317 Chirality : 0.044 0.155 2060 Planarity : 0.005 0.041 2442 Dihedral : 4.538 57.347 1852 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.35 % Allowed : 20.23 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.20), residues: 1648 helix: -0.09 (0.17), residues: 876 sheet: -0.66 (0.68), residues: 68 loop : -0.24 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 539 TYR 0.018 0.002 TYR A 556 PHE 0.020 0.002 PHE A 737 TRP 0.007 0.002 TRP D 139 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00652 (13948) covalent geometry : angle 0.60731 (18832) hydrogen bonds : bond 0.05679 ( 624) hydrogen bonds : angle 4.67601 ( 1740) metal coordination : bond 0.01055 ( 16) metal coordination : angle 4.32351 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 369 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7774 (tp) cc_final: 0.7472 (tp) REVERT: D 62 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7627 (mtt90) REVERT: C 268 GLU cc_start: 0.8099 (tt0) cc_final: 0.7462 (tm-30) REVERT: C 270 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7322 (t0) REVERT: C 349 TYR cc_start: 0.8564 (t80) cc_final: 0.8286 (t80) REVERT: C 377 MET cc_start: 0.8792 (mtt) cc_final: 0.8574 (mtt) REVERT: C 426 ASP cc_start: 0.7710 (t0) cc_final: 0.7350 (t0) REVERT: C 456 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7999 (mm-30) REVERT: C 457 VAL cc_start: 0.8718 (m) cc_final: 0.8309 (p) REVERT: C 459 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7253 (mm-30) REVERT: C 539 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7854 (mmm160) REVERT: C 545 MET cc_start: 0.7439 (mmt) cc_final: 0.7233 (mmp) REVERT: C 552 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8039 (mttp) REVERT: C 699 ASN cc_start: 0.7357 (p0) cc_final: 0.6838 (p0) REVERT: C 712 GLU cc_start: 0.8036 (tt0) cc_final: 0.7653 (tp30) REVERT: C 719 ASP cc_start: 0.8306 (t70) cc_final: 0.7963 (t0) REVERT: C 728 LYS cc_start: 0.8285 (mtmt) cc_final: 0.7998 (mmmm) REVERT: C 793 ILE cc_start: 0.8550 (mt) cc_final: 0.8328 (mt) REVERT: B 19 LEU cc_start: 0.7919 (tp) cc_final: 0.7572 (tp) REVERT: A 235 ASP cc_start: 0.7649 (p0) cc_final: 0.7120 (p0) REVERT: A 268 GLU cc_start: 0.8030 (tt0) cc_final: 0.7402 (tm-30) REVERT: A 270 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7076 (t70) REVERT: A 349 TYR cc_start: 0.8423 (t80) cc_final: 0.8162 (t80) REVERT: A 377 MET cc_start: 0.8585 (mtt) cc_final: 0.8336 (mtt) REVERT: A 426 ASP cc_start: 0.7598 (t0) cc_final: 0.7248 (t0) REVERT: A 429 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7187 (tt0) REVERT: A 456 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7931 (mm-30) REVERT: A 457 VAL cc_start: 0.8681 (m) cc_final: 0.8247 (p) REVERT: A 459 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7185 (mm-30) REVERT: A 525 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8493 (mt) REVERT: A 539 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7857 (mmm160) REVERT: A 552 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8080 (mmtm) REVERT: A 595 SER cc_start: 0.8523 (t) cc_final: 0.8265 (p) REVERT: A 635 MET cc_start: 0.8482 (tpp) cc_final: 0.8248 (tpp) REVERT: A 699 ASN cc_start: 0.7550 (p0) cc_final: 0.7211 (p0) REVERT: A 728 LYS cc_start: 0.8290 (mtmt) cc_final: 0.8018 (mtpp) REVERT: A 793 ILE cc_start: 0.8567 (mt) cc_final: 0.8360 (mt) outliers start: 36 outliers final: 23 residues processed: 390 average time/residue: 0.1360 time to fit residues: 71.6529 Evaluate side-chains 377 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 349 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 649 ARG Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 762 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 760 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 101 optimal weight: 4.9990 chunk 91 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN A 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114712 restraints weight = 19631.088| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.31 r_work: 0.3258 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2089 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= 0.137 Angle : 0.514 7.985 18856 Z= 0.261 Chirality : 0.040 0.130 2060 Planarity : 0.004 0.039 2442 Dihedral : 4.174 57.317 1848 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.42 % Allowed : 20.76 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.21), residues: 1648 helix: 0.32 (0.18), residues: 890 sheet: -0.75 (0.67), residues: 68 loop : -0.16 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 803 TYR 0.012 0.001 TYR D 77 PHE 0.019 0.001 PHE C 475 TRP 0.005 0.001 TRP B 139 HIS 0.003 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00322 (13948) covalent geometry : angle 0.50270 (18832) hydrogen bonds : bond 0.04368 ( 624) hydrogen bonds : angle 4.23366 ( 1740) metal coordination : bond 0.00451 ( 16) metal coordination : angle 3.10055 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 366 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7704 (tp) cc_final: 0.7405 (tp) REVERT: D 62 ARG cc_start: 0.7876 (mtt-85) cc_final: 0.7582 (mtt90) REVERT: C 138 GLU cc_start: 0.7387 (tp30) cc_final: 0.7153 (tp30) REVERT: C 235 ASP cc_start: 0.7400 (p0) cc_final: 0.6702 (p0) REVERT: C 268 GLU cc_start: 0.8129 (tt0) cc_final: 0.7546 (tm-30) REVERT: C 349 TYR cc_start: 0.8548 (t80) cc_final: 0.8274 (t80) REVERT: C 426 ASP cc_start: 0.7681 (t0) cc_final: 0.7303 (t0) REVERT: C 456 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7911 (mm-30) REVERT: C 457 VAL cc_start: 0.8685 (m) cc_final: 0.8276 (p) REVERT: C 459 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7164 (mm-30) REVERT: C 541 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7600 (mp0) REVERT: C 552 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8038 (mttm) REVERT: C 595 SER cc_start: 0.8641 (t) cc_final: 0.8320 (p) REVERT: C 699 ASN cc_start: 0.7344 (p0) cc_final: 0.6875 (p0) REVERT: C 719 ASP cc_start: 0.8230 (t70) cc_final: 0.7879 (t0) REVERT: C 728 LYS cc_start: 0.8184 (mtmt) cc_final: 0.7909 (mmmm) REVERT: C 793 ILE cc_start: 0.8478 (mt) cc_final: 0.8186 (mt) REVERT: B 19 LEU cc_start: 0.7833 (tp) cc_final: 0.7507 (tp) REVERT: B 93 THR cc_start: 0.7663 (OUTLIER) cc_final: 0.7279 (p) REVERT: A 134 TYR cc_start: 0.7874 (m-10) cc_final: 0.7325 (m-10) REVERT: A 235 ASP cc_start: 0.7528 (p0) cc_final: 0.6901 (p0) REVERT: A 268 GLU cc_start: 0.7994 (tt0) cc_final: 0.7322 (tm-30) REVERT: A 270 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7121 (t0) REVERT: A 276 VAL cc_start: 0.8005 (m) cc_final: 0.7781 (m) REVERT: A 349 TYR cc_start: 0.8435 (t80) cc_final: 0.8135 (t80) REVERT: A 426 ASP cc_start: 0.7604 (t0) cc_final: 0.7213 (t0) REVERT: A 429 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7169 (tt0) REVERT: A 456 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7852 (mm-30) REVERT: A 457 VAL cc_start: 0.8611 (m) cc_final: 0.8192 (p) REVERT: A 459 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7168 (mm-30) REVERT: A 525 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 595 SER cc_start: 0.8512 (t) cc_final: 0.8183 (p) REVERT: A 635 MET cc_start: 0.8484 (tpp) cc_final: 0.8247 (tpp) REVERT: A 667 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7749 (mt-10) REVERT: A 699 ASN cc_start: 0.7544 (p0) cc_final: 0.7252 (p0) REVERT: A 715 ASN cc_start: 0.8203 (m-40) cc_final: 0.7956 (m-40) REVERT: A 728 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7978 (mtpp) REVERT: A 793 ILE cc_start: 0.8533 (mt) cc_final: 0.8248 (mt) outliers start: 37 outliers final: 22 residues processed: 383 average time/residue: 0.1488 time to fit residues: 76.2656 Evaluate side-chains 371 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 345 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 762 SER Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 649 ARG Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 762 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 141 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 ASN C 321 GLN C 410 GLN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.136804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113873 restraints weight = 19651.850| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.39 r_work: 0.3258 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13964 Z= 0.138 Angle : 0.502 7.720 18856 Z= 0.253 Chirality : 0.040 0.130 2060 Planarity : 0.003 0.037 2442 Dihedral : 4.063 54.937 1848 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.42 % Allowed : 21.34 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.21), residues: 1648 helix: 0.53 (0.18), residues: 894 sheet: -0.81 (0.67), residues: 68 loop : -0.12 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 62 TYR 0.013 0.001 TYR D 77 PHE 0.020 0.001 PHE A 475 TRP 0.004 0.001 TRP B 139 HIS 0.002 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00328 (13948) covalent geometry : angle 0.49141 (18832) hydrogen bonds : bond 0.04053 ( 624) hydrogen bonds : angle 4.08013 ( 1740) metal coordination : bond 0.00474 ( 16) metal coordination : angle 2.97221 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 356 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7680 (tp) cc_final: 0.7385 (tp) REVERT: C 138 GLU cc_start: 0.7400 (tp30) cc_final: 0.7095 (tp30) REVERT: C 165 GLN cc_start: 0.8324 (mp10) cc_final: 0.7969 (mp10) REVERT: C 241 ARG cc_start: 0.8016 (ptp90) cc_final: 0.7677 (mtm110) REVERT: C 268 GLU cc_start: 0.8179 (tt0) cc_final: 0.7560 (tm-30) REVERT: C 349 TYR cc_start: 0.8559 (t80) cc_final: 0.8308 (t80) REVERT: C 426 ASP cc_start: 0.7632 (t0) cc_final: 0.7254 (t0) REVERT: C 456 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7915 (mm-30) REVERT: C 457 VAL cc_start: 0.8675 (m) cc_final: 0.8251 (p) REVERT: C 459 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7193 (mm-30) REVERT: C 537 LEU cc_start: 0.8211 (tp) cc_final: 0.7722 (tp) REVERT: C 541 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7489 (mp0) REVERT: C 552 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8035 (mttm) REVERT: C 595 SER cc_start: 0.8674 (t) cc_final: 0.8340 (p) REVERT: C 699 ASN cc_start: 0.7358 (p0) cc_final: 0.6955 (p0) REVERT: C 719 ASP cc_start: 0.8209 (t70) cc_final: 0.7859 (t0) REVERT: C 793 ILE cc_start: 0.8449 (mt) cc_final: 0.8095 (mt) REVERT: B 19 LEU cc_start: 0.7806 (tp) cc_final: 0.7478 (tp) REVERT: B 93 THR cc_start: 0.7624 (OUTLIER) cc_final: 0.7241 (p) REVERT: A 134 TYR cc_start: 0.7930 (m-10) cc_final: 0.7340 (m-10) REVERT: A 235 ASP cc_start: 0.7502 (p0) cc_final: 0.6865 (p0) REVERT: A 268 GLU cc_start: 0.8026 (tt0) cc_final: 0.7305 (tm-30) REVERT: A 349 TYR cc_start: 0.8412 (t80) cc_final: 0.8097 (t80) REVERT: A 426 ASP cc_start: 0.7660 (t0) cc_final: 0.7324 (t0) REVERT: A 429 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7172 (tt0) REVERT: A 456 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7836 (mm-30) REVERT: A 457 VAL cc_start: 0.8596 (m) cc_final: 0.8180 (p) REVERT: A 459 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7135 (mm-30) REVERT: A 525 LEU cc_start: 0.8614 (mt) cc_final: 0.8355 (mp) REVERT: A 552 LYS cc_start: 0.8365 (mmtm) cc_final: 0.8072 (mttp) REVERT: A 595 SER cc_start: 0.8491 (t) cc_final: 0.8162 (p) REVERT: A 635 MET cc_start: 0.8485 (tpp) cc_final: 0.8227 (tpp) REVERT: A 667 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 699 ASN cc_start: 0.7523 (p0) cc_final: 0.7229 (p0) REVERT: A 712 GLU cc_start: 0.7754 (tt0) cc_final: 0.7541 (tt0) REVERT: A 719 ASP cc_start: 0.7998 (t70) cc_final: 0.7684 (t0) REVERT: A 728 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7953 (mtpp) REVERT: A 793 ILE cc_start: 0.8459 (mt) cc_final: 0.8143 (mt) outliers start: 37 outliers final: 26 residues processed: 379 average time/residue: 0.1569 time to fit residues: 79.2498 Evaluate side-chains 373 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 345 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 762 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 108 optimal weight: 0.8980 chunk 79 optimal weight: 0.0170 chunk 124 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 159 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 38 optimal weight: 0.0570 chunk 139 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 ASN C 321 GLN A 321 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.139217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116549 restraints weight = 19632.231| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.36 r_work: 0.3289 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13964 Z= 0.091 Angle : 0.468 6.792 18856 Z= 0.236 Chirality : 0.038 0.122 2060 Planarity : 0.003 0.036 2442 Dihedral : 3.667 16.151 1846 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.63 % Allowed : 22.52 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.21), residues: 1648 helix: 0.82 (0.18), residues: 894 sheet: -1.05 (0.63), residues: 72 loop : -0.01 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 62 TYR 0.013 0.001 TYR C 694 PHE 0.020 0.001 PHE C 475 TRP 0.004 0.001 TRP D 139 HIS 0.001 0.000 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00202 (13948) covalent geometry : angle 0.45831 (18832) hydrogen bonds : bond 0.03360 ( 624) hydrogen bonds : angle 3.89690 ( 1740) metal coordination : bond 0.00210 ( 16) metal coordination : angle 2.71644 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 353 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7673 (tp) cc_final: 0.7398 (tp) REVERT: D 75 LYS cc_start: 0.8583 (mttp) cc_final: 0.8368 (mttp) REVERT: D 93 THR cc_start: 0.7615 (OUTLIER) cc_final: 0.7253 (p) REVERT: D 124 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7655 (ttp-110) REVERT: C 138 GLU cc_start: 0.7367 (tp30) cc_final: 0.6964 (tp30) REVERT: C 165 GLN cc_start: 0.8284 (mp10) cc_final: 0.7910 (mp10) REVERT: C 241 ARG cc_start: 0.7962 (ptp90) cc_final: 0.7662 (mtm110) REVERT: C 268 GLU cc_start: 0.8197 (tt0) cc_final: 0.7544 (tm-30) REVERT: C 291 MET cc_start: 0.7648 (mmm) cc_final: 0.7393 (mmm) REVERT: C 349 TYR cc_start: 0.8560 (t80) cc_final: 0.8278 (t80) REVERT: C 426 ASP cc_start: 0.7567 (t0) cc_final: 0.7201 (t70) REVERT: C 456 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7890 (mm-30) REVERT: C 457 VAL cc_start: 0.8683 (m) cc_final: 0.8265 (p) REVERT: C 459 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7166 (mm-30) REVERT: C 541 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7423 (mp0) REVERT: C 552 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7983 (mttp) REVERT: C 595 SER cc_start: 0.8646 (t) cc_final: 0.8332 (p) REVERT: C 699 ASN cc_start: 0.7295 (p0) cc_final: 0.6918 (p0) REVERT: C 719 ASP cc_start: 0.8128 (t70) cc_final: 0.7777 (t0) REVERT: C 793 ILE cc_start: 0.8428 (mt) cc_final: 0.8054 (mt) REVERT: B 19 LEU cc_start: 0.7808 (tp) cc_final: 0.7503 (tp) REVERT: B 124 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7699 (ttp-110) REVERT: A 134 TYR cc_start: 0.7911 (m-10) cc_final: 0.7322 (m-10) REVERT: A 235 ASP cc_start: 0.7433 (p0) cc_final: 0.6726 (p0) REVERT: A 268 GLU cc_start: 0.8024 (tt0) cc_final: 0.7315 (tm-30) REVERT: A 291 MET cc_start: 0.7835 (mmm) cc_final: 0.7543 (mmm) REVERT: A 349 TYR cc_start: 0.8396 (t80) cc_final: 0.8084 (t80) REVERT: A 354 ASN cc_start: 0.7980 (m-40) cc_final: 0.7632 (m-40) REVERT: A 387 GLU cc_start: 0.7658 (mt-10) cc_final: 0.6887 (pt0) REVERT: A 426 ASP cc_start: 0.7637 (t0) cc_final: 0.7292 (t0) REVERT: A 429 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7239 (tt0) REVERT: A 441 LYS cc_start: 0.8533 (tptp) cc_final: 0.7980 (tptm) REVERT: A 456 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7814 (mm-30) REVERT: A 457 VAL cc_start: 0.8584 (m) cc_final: 0.8154 (p) REVERT: A 459 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7129 (mm-30) REVERT: A 525 LEU cc_start: 0.8628 (mt) cc_final: 0.8383 (mp) REVERT: A 552 LYS cc_start: 0.8296 (mmtm) cc_final: 0.7932 (mttp) REVERT: A 595 SER cc_start: 0.8470 (t) cc_final: 0.8141 (p) REVERT: A 635 MET cc_start: 0.8532 (tpp) cc_final: 0.8292 (tpp) REVERT: A 667 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7762 (mt-10) REVERT: A 699 ASN cc_start: 0.7455 (p0) cc_final: 0.7186 (p0) REVERT: A 712 GLU cc_start: 0.7718 (tt0) cc_final: 0.7492 (tt0) REVERT: A 719 ASP cc_start: 0.7958 (t70) cc_final: 0.7636 (t0) REVERT: A 728 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7918 (mtpp) REVERT: A 763 ARG cc_start: 0.8250 (tpt170) cc_final: 0.8042 (tpp-160) REVERT: A 793 ILE cc_start: 0.8421 (mt) cc_final: 0.8065 (mt) outliers start: 25 outliers final: 17 residues processed: 366 average time/residue: 0.1635 time to fit residues: 79.1181 Evaluate side-chains 366 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 345 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 762 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 ASN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117339 restraints weight = 19339.894| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.24 r_work: 0.3278 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13964 Z= 0.164 Angle : 0.509 6.171 18856 Z= 0.257 Chirality : 0.041 0.131 2060 Planarity : 0.003 0.034 2442 Dihedral : 3.819 17.690 1846 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.61 % Allowed : 21.93 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.21), residues: 1648 helix: 0.73 (0.18), residues: 896 sheet: -0.91 (0.67), residues: 68 loop : -0.03 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 62 TYR 0.013 0.001 TYR D 77 PHE 0.027 0.001 PHE C 475 TRP 0.004 0.001 TRP B 139 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00395 (13948) covalent geometry : angle 0.49636 (18832) hydrogen bonds : bond 0.04114 ( 624) hydrogen bonds : angle 4.01824 ( 1740) metal coordination : bond 0.00641 ( 16) metal coordination : angle 3.13605 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 350 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7649 (tp) cc_final: 0.7327 (tp) REVERT: D 28 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7493 (t) REVERT: D 93 THR cc_start: 0.7564 (OUTLIER) cc_final: 0.7326 (p) REVERT: D 112 ASN cc_start: 0.8555 (m-40) cc_final: 0.8281 (m-40) REVERT: D 124 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7627 (ttp-110) REVERT: C 138 GLU cc_start: 0.7380 (tp30) cc_final: 0.6978 (tp30) REVERT: C 165 GLN cc_start: 0.8280 (mp10) cc_final: 0.7882 (mp10) REVERT: C 241 ARG cc_start: 0.7950 (ptp90) cc_final: 0.7714 (mtm110) REVERT: C 268 GLU cc_start: 0.8197 (tt0) cc_final: 0.7517 (tm-30) REVERT: C 291 MET cc_start: 0.7622 (mmm) cc_final: 0.7416 (mmm) REVERT: C 349 TYR cc_start: 0.8547 (t80) cc_final: 0.8228 (t80) REVERT: C 426 ASP cc_start: 0.7643 (t0) cc_final: 0.7242 (t70) REVERT: C 456 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7871 (mm-30) REVERT: C 457 VAL cc_start: 0.8616 (m) cc_final: 0.8178 (p) REVERT: C 459 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7138 (mm-30) REVERT: C 552 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7926 (mttp) REVERT: C 595 SER cc_start: 0.8674 (t) cc_final: 0.8334 (p) REVERT: C 699 ASN cc_start: 0.7383 (p0) cc_final: 0.6972 (p0) REVERT: C 719 ASP cc_start: 0.8119 (t70) cc_final: 0.7773 (t0) REVERT: C 793 ILE cc_start: 0.8398 (mt) cc_final: 0.8028 (mt) REVERT: B 19 LEU cc_start: 0.7768 (tp) cc_final: 0.7431 (tp) REVERT: B 93 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7201 (p) REVERT: B 124 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7672 (ttp-110) REVERT: A 235 ASP cc_start: 0.7388 (p0) cc_final: 0.6763 (p0) REVERT: A 268 GLU cc_start: 0.7969 (tt0) cc_final: 0.7320 (tm-30) REVERT: A 291 MET cc_start: 0.7713 (mmm) cc_final: 0.7396 (mmm) REVERT: A 349 TYR cc_start: 0.8371 (t80) cc_final: 0.8074 (t80) REVERT: A 426 ASP cc_start: 0.7639 (t0) cc_final: 0.7273 (t70) REVERT: A 429 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7159 (tt0) REVERT: A 456 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7785 (mm-30) REVERT: A 457 VAL cc_start: 0.8541 (m) cc_final: 0.8080 (p) REVERT: A 459 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7047 (mm-30) REVERT: A 525 LEU cc_start: 0.8530 (mt) cc_final: 0.8288 (mp) REVERT: A 552 LYS cc_start: 0.8308 (mmtm) cc_final: 0.8063 (mttp) REVERT: A 595 SER cc_start: 0.8472 (t) cc_final: 0.8142 (p) REVERT: A 635 MET cc_start: 0.8476 (tpp) cc_final: 0.8226 (tpp) REVERT: A 667 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7761 (mt-10) REVERT: A 699 ASN cc_start: 0.7500 (p0) cc_final: 0.7276 (p0) REVERT: A 712 GLU cc_start: 0.7699 (tt0) cc_final: 0.7469 (tt0) REVERT: A 728 LYS cc_start: 0.8188 (mtmt) cc_final: 0.7911 (mtpp) REVERT: A 747 LYS cc_start: 0.8730 (mttm) cc_final: 0.8505 (mmmt) REVERT: A 793 ILE cc_start: 0.8419 (mt) cc_final: 0.8084 (mt) outliers start: 40 outliers final: 24 residues processed: 376 average time/residue: 0.1543 time to fit residues: 77.3514 Evaluate side-chains 373 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 343 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 762 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 760 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 116 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 131 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 109 optimal weight: 0.1980 chunk 35 optimal weight: 0.0470 chunk 86 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN A 321 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.139262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116997 restraints weight = 19424.163| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.28 r_work: 0.3339 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13964 Z= 0.106 Angle : 0.488 9.185 18856 Z= 0.246 Chirality : 0.039 0.124 2060 Planarity : 0.003 0.036 2442 Dihedral : 3.700 16.520 1846 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.35 % Allowed : 22.45 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.21), residues: 1648 helix: 0.97 (0.18), residues: 888 sheet: -0.84 (0.67), residues: 68 loop : 0.08 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 62 TYR 0.014 0.001 TYR A 694 PHE 0.023 0.001 PHE C 475 TRP 0.003 0.001 TRP D 139 HIS 0.002 0.000 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00245 (13948) covalent geometry : angle 0.47811 (18832) hydrogen bonds : bond 0.03489 ( 624) hydrogen bonds : angle 3.88869 ( 1740) metal coordination : bond 0.00295 ( 16) metal coordination : angle 2.77974 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 350 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7753 (tp) cc_final: 0.7472 (tp) REVERT: D 93 THR cc_start: 0.7665 (OUTLIER) cc_final: 0.7428 (p) REVERT: D 112 ASN cc_start: 0.8622 (m-40) cc_final: 0.8400 (m-40) REVERT: D 124 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7736 (ttp-110) REVERT: C 134 TYR cc_start: 0.7781 (m-10) cc_final: 0.7553 (m-80) REVERT: C 138 GLU cc_start: 0.7355 (tp30) cc_final: 0.6936 (tp30) REVERT: C 165 GLN cc_start: 0.8330 (mp10) cc_final: 0.7951 (mp10) REVERT: C 241 ARG cc_start: 0.7991 (ptp90) cc_final: 0.7760 (mtm110) REVERT: C 268 GLU cc_start: 0.8157 (tt0) cc_final: 0.7582 (tm-30) REVERT: C 292 GLU cc_start: 0.8035 (tp30) cc_final: 0.7636 (tm-30) REVERT: C 349 TYR cc_start: 0.8590 (t80) cc_final: 0.8339 (t80) REVERT: C 426 ASP cc_start: 0.7575 (t0) cc_final: 0.7223 (t70) REVERT: C 456 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7958 (mm-30) REVERT: C 457 VAL cc_start: 0.8724 (m) cc_final: 0.8310 (p) REVERT: C 459 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7154 (mm-30) REVERT: C 541 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7507 (mm-30) REVERT: C 552 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8003 (mttp) REVERT: C 595 SER cc_start: 0.8683 (t) cc_final: 0.8362 (p) REVERT: C 699 ASN cc_start: 0.7386 (p0) cc_final: 0.7001 (p0) REVERT: C 719 ASP cc_start: 0.8148 (t70) cc_final: 0.7805 (t0) REVERT: C 793 ILE cc_start: 0.8475 (mt) cc_final: 0.8100 (mt) REVERT: B 19 LEU cc_start: 0.7865 (tp) cc_final: 0.7558 (tp) REVERT: B 124 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7749 (ttp-110) REVERT: A 134 TYR cc_start: 0.7871 (m-10) cc_final: 0.7628 (m-10) REVERT: A 140 CYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7420 (t) REVERT: A 235 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.6706 (p0) REVERT: A 268 GLU cc_start: 0.8001 (tt0) cc_final: 0.7420 (tm-30) REVERT: A 291 MET cc_start: 0.7739 (mmm) cc_final: 0.7395 (mmm) REVERT: A 349 TYR cc_start: 0.8458 (t80) cc_final: 0.8175 (t80) REVERT: A 426 ASP cc_start: 0.7560 (t0) cc_final: 0.7226 (t70) REVERT: A 429 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7220 (tt0) REVERT: A 456 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7881 (mm-30) REVERT: A 457 VAL cc_start: 0.8649 (m) cc_final: 0.8222 (p) REVERT: A 459 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7108 (mm-30) REVERT: A 525 LEU cc_start: 0.8634 (mt) cc_final: 0.8413 (mp) REVERT: A 552 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8089 (mmtp) REVERT: A 595 SER cc_start: 0.8508 (t) cc_final: 0.8184 (p) REVERT: A 667 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7733 (mt-10) REVERT: A 712 GLU cc_start: 0.7764 (tt0) cc_final: 0.7530 (tt0) REVERT: A 728 LYS cc_start: 0.8244 (mtmt) cc_final: 0.8005 (mtpp) REVERT: A 747 LYS cc_start: 0.8742 (mttm) cc_final: 0.8520 (mmmt) REVERT: A 763 ARG cc_start: 0.8273 (tpt170) cc_final: 0.7704 (mpt180) REVERT: A 793 ILE cc_start: 0.8498 (mt) cc_final: 0.8139 (mt) outliers start: 36 outliers final: 23 residues processed: 369 average time/residue: 0.1642 time to fit residues: 80.2940 Evaluate side-chains 376 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 347 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 762 SER Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 760 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 51 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 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 130 GLN C 321 GLN A 321 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.138685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117258 restraints weight = 19579.560| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.18 r_work: 0.3280 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13964 Z= 0.146 Angle : 0.514 10.436 18856 Z= 0.258 Chirality : 0.040 0.137 2060 Planarity : 0.003 0.035 2442 Dihedral : 3.771 17.223 1846 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.35 % Allowed : 22.19 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.21), residues: 1648 helix: 0.97 (0.18), residues: 892 sheet: -0.83 (0.67), residues: 68 loop : 0.03 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 62 TYR 0.015 0.001 TYR A 694 PHE 0.026 0.001 PHE C 475 TRP 0.004 0.001 TRP B 139 HIS 0.003 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00350 (13948) covalent geometry : angle 0.50326 (18832) hydrogen bonds : bond 0.03873 ( 624) hydrogen bonds : angle 3.93862 ( 1740) metal coordination : bond 0.00551 ( 16) metal coordination : angle 2.97823 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 349 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7633 (tp) cc_final: 0.7330 (tp) REVERT: D 93 THR cc_start: 0.7618 (OUTLIER) cc_final: 0.7375 (p) REVERT: D 112 ASN cc_start: 0.8579 (m-40) cc_final: 0.8375 (m-40) REVERT: D 124 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7656 (ttp-110) REVERT: C 134 TYR cc_start: 0.7810 (m-10) cc_final: 0.7580 (m-80) REVERT: C 138 GLU cc_start: 0.7337 (tp30) cc_final: 0.6876 (tp30) REVERT: C 165 GLN cc_start: 0.8334 (mp10) cc_final: 0.7925 (mp10) REVERT: C 241 ARG cc_start: 0.7937 (ptp90) cc_final: 0.7718 (mtm110) REVERT: C 268 GLU cc_start: 0.8140 (tt0) cc_final: 0.7556 (tm-30) REVERT: C 292 GLU cc_start: 0.8113 (tp30) cc_final: 0.7672 (tm-30) REVERT: C 349 TYR cc_start: 0.8575 (t80) cc_final: 0.8353 (t80) REVERT: C 426 ASP cc_start: 0.7590 (t0) cc_final: 0.7238 (t70) REVERT: C 456 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7939 (mm-30) REVERT: C 457 VAL cc_start: 0.8639 (m) cc_final: 0.8213 (p) REVERT: C 459 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7088 (mm-30) REVERT: C 552 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7994 (mttm) REVERT: C 595 SER cc_start: 0.8693 (t) cc_final: 0.8366 (p) REVERT: C 699 ASN cc_start: 0.7442 (p0) cc_final: 0.7028 (p0) REVERT: C 719 ASP cc_start: 0.8120 (t70) cc_final: 0.7773 (t0) REVERT: C 793 ILE cc_start: 0.8404 (mt) cc_final: 0.8037 (mt) REVERT: B 19 LEU cc_start: 0.7790 (tp) cc_final: 0.7453 (tp) REVERT: B 99 TYR cc_start: 0.8215 (m-80) cc_final: 0.7480 (m-80) REVERT: B 124 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7716 (ttp-110) REVERT: A 134 TYR cc_start: 0.7916 (m-10) cc_final: 0.7659 (m-10) REVERT: A 140 CYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7433 (t) REVERT: A 235 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.6785 (p0) REVERT: A 268 GLU cc_start: 0.7957 (tt0) cc_final: 0.7370 (tm-30) REVERT: A 291 MET cc_start: 0.7685 (mmm) cc_final: 0.7342 (mmm) REVERT: A 349 TYR cc_start: 0.8334 (t80) cc_final: 0.8076 (t80) REVERT: A 387 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6807 (pt0) REVERT: A 426 ASP cc_start: 0.7535 (t0) cc_final: 0.7187 (t70) REVERT: A 429 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7193 (tt0) REVERT: A 441 LYS cc_start: 0.8467 (tptm) cc_final: 0.8032 (tptp) REVERT: A 456 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7871 (mm-30) REVERT: A 457 VAL cc_start: 0.8592 (m) cc_final: 0.8148 (p) REVERT: A 459 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7003 (mm-30) REVERT: A 525 LEU cc_start: 0.8607 (mt) cc_final: 0.8357 (mp) REVERT: A 552 LYS cc_start: 0.8416 (mmtm) cc_final: 0.8107 (mmtp) REVERT: A 595 SER cc_start: 0.8500 (t) cc_final: 0.8177 (p) REVERT: A 667 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7713 (mt-10) REVERT: A 712 GLU cc_start: 0.7737 (tt0) cc_final: 0.7494 (tt0) REVERT: A 728 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7988 (mtpp) REVERT: A 747 LYS cc_start: 0.8675 (mttm) cc_final: 0.8435 (mmmt) REVERT: A 763 ARG cc_start: 0.8239 (tpt170) cc_final: 0.7692 (mpt180) REVERT: A 793 ILE cc_start: 0.8447 (mt) cc_final: 0.8117 (mt) outliers start: 36 outliers final: 27 residues processed: 374 average time/residue: 0.1562 time to fit residues: 78.0171 Evaluate side-chains 378 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 345 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 760 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 154 optimal weight: 3.9990 chunk 71 optimal weight: 0.0970 chunk 122 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN A 335 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.140886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118920 restraints weight = 19423.931| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.25 r_work: 0.3331 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13964 Z= 0.121 Angle : 0.507 11.071 18856 Z= 0.252 Chirality : 0.039 0.131 2060 Planarity : 0.003 0.036 2442 Dihedral : 3.705 16.582 1846 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.35 % Allowed : 22.45 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.21), residues: 1648 helix: 1.06 (0.18), residues: 890 sheet: -0.81 (0.67), residues: 68 loop : 0.10 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 62 TYR 0.016 0.001 TYR A 694 PHE 0.025 0.001 PHE C 475 TRP 0.004 0.001 TRP A 328 HIS 0.002 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00286 (13948) covalent geometry : angle 0.49747 (18832) hydrogen bonds : bond 0.03586 ( 624) hydrogen bonds : angle 3.88085 ( 1740) metal coordination : bond 0.00384 ( 16) metal coordination : angle 2.84594 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 345 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7763 (tp) cc_final: 0.7480 (tp) REVERT: D 93 THR cc_start: 0.7672 (OUTLIER) cc_final: 0.7438 (p) REVERT: D 124 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7736 (ttp-110) REVERT: D 136 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8198 (mtp85) REVERT: C 134 TYR cc_start: 0.7775 (m-10) cc_final: 0.7534 (m-80) REVERT: C 165 GLN cc_start: 0.8328 (mp10) cc_final: 0.7935 (mp10) REVERT: C 241 ARG cc_start: 0.7902 (ptp90) cc_final: 0.7630 (mtm110) REVERT: C 268 GLU cc_start: 0.8127 (tt0) cc_final: 0.7665 (tm-30) REVERT: C 349 TYR cc_start: 0.8560 (t80) cc_final: 0.8336 (t80) REVERT: C 426 ASP cc_start: 0.7575 (t0) cc_final: 0.7261 (t70) REVERT: C 456 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7975 (mm-30) REVERT: C 457 VAL cc_start: 0.8721 (m) cc_final: 0.8301 (p) REVERT: C 459 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7149 (mm-30) REVERT: C 541 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7519 (mm-30) REVERT: C 552 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8031 (mttm) REVERT: C 595 SER cc_start: 0.8691 (t) cc_final: 0.8372 (p) REVERT: C 699 ASN cc_start: 0.7426 (p0) cc_final: 0.7046 (p0) REVERT: C 719 ASP cc_start: 0.8115 (t70) cc_final: 0.7778 (t0) REVERT: C 793 ILE cc_start: 0.8461 (mt) cc_final: 0.8107 (mt) REVERT: B 19 LEU cc_start: 0.7890 (tp) cc_final: 0.7570 (tp) REVERT: B 93 THR cc_start: 0.7660 (OUTLIER) cc_final: 0.7284 (p) REVERT: B 99 TYR cc_start: 0.8243 (m-80) cc_final: 0.7516 (m-80) REVERT: B 124 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7768 (ttp-110) REVERT: A 134 TYR cc_start: 0.7885 (m-10) cc_final: 0.7630 (m-10) REVERT: A 140 CYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7433 (t) REVERT: A 235 ASP cc_start: 0.7368 (p0) cc_final: 0.6828 (p0) REVERT: A 268 GLU cc_start: 0.7920 (tt0) cc_final: 0.7474 (tm-30) REVERT: A 291 MET cc_start: 0.7651 (mmm) cc_final: 0.7285 (mmm) REVERT: A 349 TYR cc_start: 0.8365 (t80) cc_final: 0.8102 (t80) REVERT: A 387 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6825 (pt0) REVERT: A 426 ASP cc_start: 0.7535 (t0) cc_final: 0.7225 (t70) REVERT: A 429 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7245 (tt0) REVERT: A 441 LYS cc_start: 0.8560 (tptm) cc_final: 0.8139 (tptp) REVERT: A 456 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7899 (mm-30) REVERT: A 457 VAL cc_start: 0.8645 (m) cc_final: 0.8219 (p) REVERT: A 459 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7029 (mm-30) REVERT: A 552 LYS cc_start: 0.8398 (mmtm) cc_final: 0.8091 (mmtp) REVERT: A 595 SER cc_start: 0.8511 (t) cc_final: 0.8193 (p) REVERT: A 667 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7738 (mt-10) REVERT: A 712 GLU cc_start: 0.7726 (tt0) cc_final: 0.7477 (tt0) REVERT: A 728 LYS cc_start: 0.8274 (mtmt) cc_final: 0.8026 (mtpp) REVERT: A 747 LYS cc_start: 0.8722 (mttm) cc_final: 0.8497 (mmmt) REVERT: A 763 ARG cc_start: 0.8305 (tpt170) cc_final: 0.7762 (mpt180) REVERT: A 793 ILE cc_start: 0.8527 (mt) cc_final: 0.8202 (mt) outliers start: 36 outliers final: 27 residues processed: 368 average time/residue: 0.1645 time to fit residues: 80.9587 Evaluate side-chains 374 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 340 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 136 ARG Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 760 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 35 optimal weight: 0.4980 chunk 132 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 0.0010 chunk 69 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 75 optimal weight: 0.0040 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN B 130 GLN A 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.140588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119303 restraints weight = 19569.162| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.22 r_work: 0.3352 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13964 Z= 0.093 Angle : 0.490 11.643 18856 Z= 0.244 Chirality : 0.038 0.131 2060 Planarity : 0.003 0.037 2442 Dihedral : 3.579 15.288 1846 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.96 % Allowed : 23.30 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.21), residues: 1648 helix: 1.17 (0.18), residues: 904 sheet: -0.86 (0.66), residues: 68 loop : -0.03 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 539 TYR 0.018 0.001 TYR A 694 PHE 0.025 0.001 PHE C 475 TRP 0.004 0.001 TRP D 139 HIS 0.001 0.000 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00211 (13948) covalent geometry : angle 0.48011 (18832) hydrogen bonds : bond 0.03157 ( 624) hydrogen bonds : angle 3.78425 ( 1740) metal coordination : bond 0.00231 ( 16) metal coordination : angle 2.77854 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 348 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7699 (tp) cc_final: 0.7446 (tp) REVERT: D 75 LYS cc_start: 0.8632 (mttp) cc_final: 0.8380 (mttp) REVERT: D 93 THR cc_start: 0.7685 (OUTLIER) cc_final: 0.7325 (p) REVERT: D 99 TYR cc_start: 0.8055 (m-80) cc_final: 0.7416 (m-80) REVERT: D 124 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7652 (ttp-110) REVERT: C 134 TYR cc_start: 0.7753 (m-10) cc_final: 0.7538 (m-10) REVERT: C 165 GLN cc_start: 0.8327 (mp10) cc_final: 0.7959 (mp10) REVERT: C 241 ARG cc_start: 0.7862 (ptp90) cc_final: 0.7650 (mtm110) REVERT: C 268 GLU cc_start: 0.8074 (tt0) cc_final: 0.7669 (tm-30) REVERT: C 292 GLU cc_start: 0.7958 (tp30) cc_final: 0.7705 (tm-30) REVERT: C 313 MET cc_start: 0.8632 (ttp) cc_final: 0.8375 (ttp) REVERT: C 426 ASP cc_start: 0.7517 (t0) cc_final: 0.7222 (t70) REVERT: C 456 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7978 (mm-30) REVERT: C 457 VAL cc_start: 0.8714 (m) cc_final: 0.8315 (p) REVERT: C 459 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7076 (mm-30) REVERT: C 541 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7459 (mm-30) REVERT: C 552 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8012 (mttp) REVERT: C 595 SER cc_start: 0.8669 (t) cc_final: 0.8353 (p) REVERT: C 699 ASN cc_start: 0.7367 (p0) cc_final: 0.6995 (p0) REVERT: C 719 ASP cc_start: 0.8100 (t70) cc_final: 0.7772 (t0) REVERT: C 772 GLU cc_start: 0.8005 (tp30) cc_final: 0.7575 (tp30) REVERT: C 793 ILE cc_start: 0.8483 (mt) cc_final: 0.8119 (mt) REVERT: B 19 LEU cc_start: 0.7883 (tp) cc_final: 0.7584 (tp) REVERT: B 99 TYR cc_start: 0.8267 (m-80) cc_final: 0.7550 (m-80) REVERT: B 124 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7687 (ttp-110) REVERT: A 134 TYR cc_start: 0.7866 (m-10) cc_final: 0.7619 (m-10) REVERT: A 140 CYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7373 (t) REVERT: A 235 ASP cc_start: 0.7302 (p0) cc_final: 0.6715 (p0) REVERT: A 268 GLU cc_start: 0.7881 (tt0) cc_final: 0.7480 (tm-30) REVERT: A 291 MET cc_start: 0.7653 (mmm) cc_final: 0.7269 (mmm) REVERT: A 309 PHE cc_start: 0.7965 (t80) cc_final: 0.7411 (t80) REVERT: A 349 TYR cc_start: 0.8367 (t80) cc_final: 0.8150 (t80) REVERT: A 426 ASP cc_start: 0.7504 (t0) cc_final: 0.7184 (t70) REVERT: A 456 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7908 (mm-30) REVERT: A 457 VAL cc_start: 0.8642 (m) cc_final: 0.8226 (p) REVERT: A 459 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6939 (mm-30) REVERT: A 552 LYS cc_start: 0.8322 (mmtm) cc_final: 0.8121 (mmtm) REVERT: A 595 SER cc_start: 0.8522 (t) cc_final: 0.8207 (p) REVERT: A 667 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 712 GLU cc_start: 0.7759 (tt0) cc_final: 0.7503 (tt0) REVERT: A 747 LYS cc_start: 0.8645 (mttm) cc_final: 0.8390 (mmmt) REVERT: A 763 ARG cc_start: 0.8192 (tpt170) cc_final: 0.7686 (mpt180) REVERT: A 793 ILE cc_start: 0.8525 (mt) cc_final: 0.8177 (mt) outliers start: 30 outliers final: 22 residues processed: 367 average time/residue: 0.1705 time to fit residues: 83.1775 Evaluate side-chains 371 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 344 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 760 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 45 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 125 optimal weight: 0.0670 chunk 123 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 109 optimal weight: 0.0470 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.118279 restraints weight = 19683.465| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.31 r_work: 0.3311 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2913 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= 0.093 Angle : 0.493 12.105 18856 Z= 0.245 Chirality : 0.038 0.121 2060 Planarity : 0.003 0.036 2442 Dihedral : 3.527 14.775 1846 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.76 % Allowed : 23.83 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.21), residues: 1648 helix: 1.11 (0.18), residues: 924 sheet: -1.05 (0.62), residues: 72 loop : -0.07 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 62 TYR 0.023 0.001 TYR A 694 PHE 0.028 0.001 PHE A 475 TRP 0.004 0.001 TRP A 328 HIS 0.001 0.000 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00210 (13948) covalent geometry : angle 0.48419 (18832) hydrogen bonds : bond 0.03067 ( 624) hydrogen bonds : angle 3.75196 ( 1740) metal coordination : bond 0.00195 ( 16) metal coordination : angle 2.71129 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4034.34 seconds wall clock time: 69 minutes 35.15 seconds (4175.15 seconds total)