Starting phenix.real_space_refine on Thu Jul 31 18:40:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jro_36600/07_2025/8jro_36600.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jro_36600/07_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_36600/07_2025/8jro_36600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jro_36600/07_2025/8jro_36600.map" model { file = "/net/cci-nas-00/data/ceres_data/8jro_36600/07_2025/8jro_36600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jro_36600/07_2025/8jro_36600.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13672 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1191 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "A" Number of atoms: 5643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5643 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 28, 'TRANS': 660} Chain breaks: 1 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7075 SG CYS B 37 62.535 33.102 92.664 1.00 49.18 S ATOM 7100 SG CYS B 40 61.587 35.867 94.938 1.00 52.17 S ATOM 7356 SG CYS B 70 60.298 35.802 91.258 1.00 54.24 S ATOM 7379 SG CYS B 73 63.790 36.769 91.996 1.00 68.14 S ATOM 7698 SG CYS B 110 62.119 35.779 74.747 1.00 60.52 S ATOM 7720 SG CYS B 113 59.976 34.499 77.528 1.00 55.65 S ATOM 7982 SG CYS B 143 58.478 35.379 74.071 1.00 71.13 S ATOM 8002 SG CYS B 146 59.602 38.155 76.387 1.00 63.68 S Restraints were copied for chains: D, C Time building chain proxies: 12.17, per 1000 atoms: 0.89 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: 3.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.46 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: 3.94 Time building geometry restraints manager: 3.71 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.160 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.010 ------------------------------------------------------------------------------- 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 : 7.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (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 TRP 0.005 0.001 TRP C 328 HIS 0.002 0.000 HIS D 31 PHE 0.012 0.001 PHE A 475 TYR 0.015 0.001 TYR B 77 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.25586 ( 624) hydrogen bonds : angle 7.65896 ( 1740) metal coordination : bond 0.00307 ( 16) metal coordination : angle 3.16739 ( 24) covalent geometry : bond 0.00347 (13948) covalent geometry : angle 0.50192 (18832) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 389 time to evaluate : 1.554 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: 0.7872 (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: 0.6645 (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: 0.3352 time to fit residues: 174.8713 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 : 1.426 ------------------------------------------------------------------------------- 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 138 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 357 ASN C 451 ASN C 715 ASN C 795 HIS C 845 ASN B 112 ASN A 321 GLN A 357 ASN A 451 ASN A 681 GLN A 715 ASN A 795 HIS A 845 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.137435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114892 restraints weight = 19542.488| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.27 r_work: 0.3302 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13964 Z= 0.166 Angle : 0.556 7.817 18856 Z= 0.284 Chirality : 0.041 0.156 2060 Planarity : 0.004 0.035 2442 Dihedral : 4.248 58.440 1852 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.50 % Allowed : 19.84 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1648 helix: 0.10 (0.17), residues: 886 sheet: -0.68 (0.69), residues: 68 loop : -0.18 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 139 HIS 0.002 0.001 HIS B 31 PHE 0.014 0.001 PHE A 797 TYR 0.016 0.001 TYR A 273 ARG 0.005 0.000 ARG C 803 Details of bonding type rmsd hydrogen bonds : bond 0.05263 ( 624) hydrogen bonds : angle 4.59484 ( 1740) metal coordination : bond 0.00575 ( 16) metal coordination : angle 3.42695 ( 24) covalent geometry : bond 0.00390 (13948) covalent geometry : angle 0.54225 (18832) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 369 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7802 (tp) cc_final: 0.7522 (tp) REVERT: D 28 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7557 (t) REVERT: D 62 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7722 (mtt90) REVERT: C 122 PHE cc_start: 0.7508 (m-80) cc_final: 0.7289 (m-10) REVERT: C 268 GLU cc_start: 0.8110 (tt0) cc_final: 0.7514 (tm-30) REVERT: C 270 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7245 (t0) REVERT: C 349 TYR cc_start: 0.8545 (t80) cc_final: 0.8313 (t80) REVERT: C 426 ASP cc_start: 0.7609 (t0) cc_final: 0.7265 (t0) REVERT: C 456 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7973 (mm-30) REVERT: C 457 VAL cc_start: 0.8791 (m) cc_final: 0.8357 (p) REVERT: C 459 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7211 (mm-30) REVERT: C 541 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7820 (mm-30) REVERT: C 552 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8095 (mttp) REVERT: C 635 MET cc_start: 0.8434 (tpp) cc_final: 0.8227 (tpp) REVERT: C 712 GLU cc_start: 0.8035 (tt0) cc_final: 0.7670 (tp30) REVERT: C 719 ASP cc_start: 0.8336 (t70) cc_final: 0.7972 (t0) REVERT: C 728 LYS cc_start: 0.8303 (mtmt) cc_final: 0.7982 (mmmm) REVERT: C 793 ILE cc_start: 0.8520 (mt) cc_final: 0.8288 (mt) REVERT: B 15 ARG cc_start: 0.7569 (ptt180) cc_final: 0.7365 (ptt180) REVERT: B 19 LEU cc_start: 0.7926 (tp) cc_final: 0.7600 (tp) REVERT: B 28 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7563 (t) REVERT: A 235 ASP cc_start: 0.7626 (p0) cc_final: 0.7101 (p0) REVERT: A 268 GLU cc_start: 0.8043 (tt0) cc_final: 0.7410 (tm-30) REVERT: A 270 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7072 (t70) REVERT: A 276 VAL cc_start: 0.8188 (m) cc_final: 0.7955 (m) REVERT: A 300 GLU cc_start: 0.8048 (pt0) cc_final: 0.7844 (pt0) REVERT: A 349 TYR cc_start: 0.8413 (t80) cc_final: 0.8038 (t80) REVERT: A 426 ASP cc_start: 0.7559 (t0) cc_final: 0.7234 (t0) REVERT: A 429 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7168 (tt0) REVERT: A 456 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7912 (mm-30) REVERT: A 457 VAL cc_start: 0.8713 (m) cc_final: 0.8267 (p) REVERT: A 459 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7169 (mm-30) REVERT: A 525 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8486 (mt) REVERT: A 539 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7768 (mmm160) REVERT: A 552 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8178 (mttp) REVERT: A 595 SER cc_start: 0.8489 (t) cc_final: 0.8252 (p) REVERT: A 635 MET cc_start: 0.8439 (tpp) cc_final: 0.8197 (tpp) REVERT: A 667 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7824 (mt-10) REVERT: A 699 ASN cc_start: 0.7411 (p0) cc_final: 0.7115 (p0) REVERT: A 714 VAL cc_start: 0.8368 (t) cc_final: 0.8165 (p) REVERT: A 715 ASN cc_start: 0.8287 (m-40) cc_final: 0.8004 (m-40) REVERT: A 728 LYS cc_start: 0.8325 (mtmt) cc_final: 0.8042 (mtpp) REVERT: A 775 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7813 (mm-30) REVERT: A 793 ILE cc_start: 0.8571 (mt) cc_final: 0.8348 (mt) outliers start: 23 outliers final: 10 residues processed: 382 average time/residue: 0.3349 time to fit residues: 171.8613 Evaluate side-chains 369 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 352 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 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 491 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 693 MET 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 A residue 251 LYS Chi-restraints excluded: chain A residue 270 ASP 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 66 optimal weight: 0.2980 chunk 139 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 ASN D 130 GLN C 321 GLN C 547 ASN A 321 GLN A 547 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115133 restraints weight = 19755.887| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.37 r_work: 0.3274 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13964 Z= 0.111 Angle : 0.495 8.141 18856 Z= 0.249 Chirality : 0.039 0.126 2060 Planarity : 0.003 0.035 2442 Dihedral : 3.971 56.988 1848 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.89 % Allowed : 20.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1648 helix: 0.47 (0.18), residues: 894 sheet: -0.74 (0.68), residues: 68 loop : -0.06 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 139 HIS 0.002 0.000 HIS A 655 PHE 0.018 0.001 PHE C 475 TYR 0.011 0.001 TYR C 694 ARG 0.005 0.000 ARG C 141 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 624) hydrogen bonds : angle 4.11245 ( 1740) metal coordination : bond 0.00345 ( 16) metal coordination : angle 2.93841 ( 24) covalent geometry : bond 0.00258 (13948) covalent geometry : angle 0.48408 (18832) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 367 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7709 (tp) cc_final: 0.7422 (tp) REVERT: D 62 ARG cc_start: 0.7852 (mtt-85) cc_final: 0.7613 (mtt90) REVERT: C 138 GLU cc_start: 0.7516 (tp30) cc_final: 0.7284 (tp30) REVERT: C 235 ASP cc_start: 0.7283 (p0) cc_final: 0.6621 (p0) REVERT: C 268 GLU cc_start: 0.8194 (tt0) cc_final: 0.7584 (tm-30) REVERT: C 349 TYR cc_start: 0.8526 (t80) cc_final: 0.8234 (t80) REVERT: C 426 ASP cc_start: 0.7672 (t0) cc_final: 0.7271 (t0) REVERT: C 456 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7892 (mm-30) REVERT: C 457 VAL cc_start: 0.8671 (m) cc_final: 0.8272 (p) REVERT: C 459 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7242 (mm-30) REVERT: C 539 ARG cc_start: 0.7833 (mmm160) cc_final: 0.7629 (mmm160) REVERT: C 541 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7677 (mm-30) REVERT: C 552 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8061 (mttp) REVERT: C 635 MET cc_start: 0.8474 (tpp) cc_final: 0.8266 (tpp) REVERT: C 719 ASP cc_start: 0.8209 (t70) cc_final: 0.7861 (t0) REVERT: C 728 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7875 (mmmm) REVERT: C 793 ILE cc_start: 0.8475 (mt) cc_final: 0.8174 (mt) REVERT: B 19 LEU cc_start: 0.7822 (tp) cc_final: 0.7512 (tp) REVERT: B 62 ARG cc_start: 0.7873 (mtt-85) cc_final: 0.7610 (mtt90) REVERT: A 235 ASP cc_start: 0.7475 (p0) cc_final: 0.6869 (p0) REVERT: A 241 ARG cc_start: 0.8115 (ptp-110) cc_final: 0.7832 (ptp-110) REVERT: A 268 GLU cc_start: 0.8105 (tt0) cc_final: 0.7385 (tm-30) REVERT: A 291 MET cc_start: 0.8035 (mmm) cc_final: 0.7678 (mmm) REVERT: A 300 GLU cc_start: 0.8140 (pt0) cc_final: 0.7939 (pt0) REVERT: A 349 TYR cc_start: 0.8425 (t80) cc_final: 0.8023 (t80) REVERT: A 426 ASP cc_start: 0.7608 (t0) cc_final: 0.7218 (t0) REVERT: A 429 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7182 (tt0) REVERT: A 456 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7845 (mm-30) REVERT: A 457 VAL cc_start: 0.8593 (m) cc_final: 0.8170 (p) REVERT: A 459 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7220 (mm-30) REVERT: A 525 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8417 (mp) REVERT: A 552 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8107 (mttp) REVERT: A 595 SER cc_start: 0.8518 (t) cc_final: 0.8242 (p) REVERT: A 635 MET cc_start: 0.8460 (tpp) cc_final: 0.8215 (tpp) REVERT: A 667 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7742 (mt-10) REVERT: A 699 ASN cc_start: 0.7410 (p0) cc_final: 0.7153 (p0) REVERT: A 712 GLU cc_start: 0.7744 (tt0) cc_final: 0.7430 (tt0) REVERT: A 728 LYS cc_start: 0.8201 (mtmt) cc_final: 0.7965 (mtpp) REVERT: A 775 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 793 ILE cc_start: 0.8505 (mt) cc_final: 0.8203 (mt) outliers start: 29 outliers final: 15 residues processed: 381 average time/residue: 0.3515 time to fit residues: 177.6469 Evaluate side-chains 377 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 359 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 552 LYS Chi-restraints excluded: chain C residue 570 VAL 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 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 415 GLU 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 570 VAL Chi-restraints excluded: chain A residue 760 CYS 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 155 optimal weight: 0.2980 chunk 115 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 0.0030 chunk 143 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 0.0570 chunk 122 optimal weight: 0.9990 overall best weight: 0.3508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 ASN D 130 GLN C 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.139166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116600 restraints weight = 19403.938| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.30 r_work: 0.3292 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13964 Z= 0.096 Angle : 0.470 7.672 18856 Z= 0.236 Chirality : 0.038 0.124 2060 Planarity : 0.003 0.035 2442 Dihedral : 3.823 55.289 1848 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.70 % Allowed : 21.80 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1648 helix: 0.79 (0.18), residues: 888 sheet: -1.08 (0.63), residues: 72 loop : -0.02 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 139 HIS 0.001 0.000 HIS C 655 PHE 0.020 0.001 PHE C 475 TYR 0.015 0.001 TYR A 262 ARG 0.005 0.000 ARG A 803 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 624) hydrogen bonds : angle 3.91523 ( 1740) metal coordination : bond 0.00270 ( 16) metal coordination : angle 2.77259 ( 24) covalent geometry : bond 0.00218 (13948) covalent geometry : angle 0.46010 (18832) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 350 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7703 (tp) cc_final: 0.7422 (tp) REVERT: C 138 GLU cc_start: 0.7488 (tp30) cc_final: 0.7144 (tp30) REVERT: C 141 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7570 (ttp80) REVERT: C 241 ARG cc_start: 0.8007 (ptp90) cc_final: 0.7624 (mtm110) REVERT: C 268 GLU cc_start: 0.8209 (tt0) cc_final: 0.7557 (tm-30) REVERT: C 349 TYR cc_start: 0.8527 (t80) cc_final: 0.8253 (t80) REVERT: C 426 ASP cc_start: 0.7636 (t0) cc_final: 0.7248 (t0) REVERT: C 456 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7877 (mm-30) REVERT: C 457 VAL cc_start: 0.8683 (m) cc_final: 0.8265 (p) REVERT: C 459 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7232 (mm-30) REVERT: C 526 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8243 (tttm) REVERT: C 541 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7647 (mm-30) REVERT: C 552 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8026 (mttp) REVERT: C 595 SER cc_start: 0.8623 (t) cc_final: 0.8302 (p) REVERT: C 635 MET cc_start: 0.8490 (tpp) cc_final: 0.8286 (tpp) REVERT: C 719 ASP cc_start: 0.8187 (t70) cc_final: 0.7842 (t0) REVERT: C 793 ILE cc_start: 0.8433 (mt) cc_final: 0.8079 (mt) REVERT: B 19 LEU cc_start: 0.7816 (tp) cc_final: 0.7512 (tp) REVERT: B 62 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.7599 (mtt90) REVERT: B 136 ARG cc_start: 0.8495 (ttt90) cc_final: 0.8251 (ttm-80) REVERT: A 235 ASP cc_start: 0.7397 (p0) cc_final: 0.6759 (p0) REVERT: A 241 ARG cc_start: 0.8085 (ptp-110) cc_final: 0.7807 (ptp-110) REVERT: A 268 GLU cc_start: 0.8102 (tt0) cc_final: 0.7408 (tm-30) REVERT: A 300 GLU cc_start: 0.8163 (pt0) cc_final: 0.7944 (pt0) REVERT: A 349 TYR cc_start: 0.8380 (t80) cc_final: 0.8084 (t80) REVERT: A 394 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7579 (tp30) REVERT: A 426 ASP cc_start: 0.7574 (t0) cc_final: 0.7194 (t0) REVERT: A 429 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7154 (tt0) REVERT: A 456 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7796 (mm-30) REVERT: A 457 VAL cc_start: 0.8593 (m) cc_final: 0.8155 (p) REVERT: A 459 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7092 (mm-30) REVERT: A 525 LEU cc_start: 0.8675 (mt) cc_final: 0.8379 (mp) REVERT: A 552 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8039 (mttp) REVERT: A 580 GLU cc_start: 0.8256 (tt0) cc_final: 0.8007 (tt0) REVERT: A 595 SER cc_start: 0.8478 (t) cc_final: 0.8140 (p) REVERT: A 635 MET cc_start: 0.8485 (tpp) cc_final: 0.8238 (tpp) REVERT: A 667 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 699 ASN cc_start: 0.7379 (p0) cc_final: 0.7141 (p0) REVERT: A 712 GLU cc_start: 0.7747 (tt0) cc_final: 0.7444 (tt0) REVERT: A 728 LYS cc_start: 0.8132 (mtmt) cc_final: 0.7907 (mtpp) REVERT: A 763 ARG cc_start: 0.8267 (tpt170) cc_final: 0.8026 (tpp-160) REVERT: A 775 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7779 (mm-30) REVERT: A 793 ILE cc_start: 0.8438 (mt) cc_final: 0.8094 (mt) outliers start: 26 outliers final: 17 residues processed: 362 average time/residue: 0.3344 time to fit residues: 161.0362 Evaluate side-chains 363 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 343 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 ILE 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 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 C residue 760 CYS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 552 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 0 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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** C 335 GLN C 392 HIS C 547 ASN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.135818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112971 restraints weight = 19780.165| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.38 r_work: 0.3292 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13964 Z= 0.198 Angle : 0.528 7.384 18856 Z= 0.264 Chirality : 0.041 0.134 2060 Planarity : 0.004 0.035 2442 Dihedral : 3.844 17.266 1846 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.48 % Allowed : 21.34 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1648 helix: 0.67 (0.18), residues: 884 sheet: -0.89 (0.66), residues: 68 loop : -0.02 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 791 HIS 0.004 0.001 HIS A 655 PHE 0.025 0.002 PHE C 475 TYR 0.020 0.002 TYR A 556 ARG 0.005 0.000 ARG C 524 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 624) hydrogen bonds : angle 4.07823 ( 1740) metal coordination : bond 0.00792 ( 16) metal coordination : angle 3.30272 ( 24) covalent geometry : bond 0.00480 (13948) covalent geometry : angle 0.51546 (18832) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 364 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7676 (tp) cc_final: 0.7366 (tp) REVERT: D 28 THR cc_start: 0.7849 (OUTLIER) cc_final: 0.7535 (t) REVERT: C 141 ARG cc_start: 0.7836 (ttp80) cc_final: 0.7445 (ttp80) REVERT: C 268 GLU cc_start: 0.7923 (tt0) cc_final: 0.7396 (tm-30) REVERT: C 349 TYR cc_start: 0.8404 (t80) cc_final: 0.8105 (t80) REVERT: C 426 ASP cc_start: 0.7445 (t0) cc_final: 0.7064 (t70) REVERT: C 456 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7721 (mm-30) REVERT: C 457 VAL cc_start: 0.8596 (m) cc_final: 0.8136 (p) REVERT: C 459 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6961 (mm-30) REVERT: C 552 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7837 (mttp) REVERT: C 595 SER cc_start: 0.8645 (t) cc_final: 0.8313 (p) REVERT: C 699 ASN cc_start: 0.7261 (p0) cc_final: 0.6900 (p0) REVERT: C 719 ASP cc_start: 0.8003 (t70) cc_final: 0.7642 (t0) REVERT: C 728 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7793 (mmmm) REVERT: C 793 ILE cc_start: 0.8422 (mt) cc_final: 0.8078 (mt) REVERT: B 19 LEU cc_start: 0.7796 (tp) cc_final: 0.7453 (tp) REVERT: B 28 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7510 (t) REVERT: B 62 ARG cc_start: 0.7798 (mtt-85) cc_final: 0.7459 (mtt90) REVERT: A 235 ASP cc_start: 0.7263 (p0) cc_final: 0.6691 (p0) REVERT: A 241 ARG cc_start: 0.8034 (ptp-110) cc_final: 0.7762 (ptp-110) REVERT: A 268 GLU cc_start: 0.7823 (tt0) cc_final: 0.7196 (tm-30) REVERT: A 291 MET cc_start: 0.7626 (mmm) cc_final: 0.7324 (mmm) REVERT: A 300 GLU cc_start: 0.7928 (pt0) cc_final: 0.7691 (pt0) REVERT: A 349 TYR cc_start: 0.8279 (t80) cc_final: 0.8023 (t80) REVERT: A 426 ASP cc_start: 0.7361 (t0) cc_final: 0.7016 (t70) REVERT: A 429 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6904 (tt0) REVERT: A 456 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7686 (mm-30) REVERT: A 457 VAL cc_start: 0.8517 (m) cc_final: 0.8060 (p) REVERT: A 459 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6881 (mm-30) REVERT: A 525 LEU cc_start: 0.8524 (mt) cc_final: 0.8252 (mp) REVERT: A 552 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7916 (mttp) REVERT: A 595 SER cc_start: 0.8515 (t) cc_final: 0.8177 (p) REVERT: A 635 MET cc_start: 0.8195 (tpp) cc_final: 0.7880 (tpp) REVERT: A 667 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 712 GLU cc_start: 0.7682 (tt0) cc_final: 0.7354 (tt0) REVERT: A 728 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7874 (mtpp) REVERT: A 793 ILE cc_start: 0.8448 (mt) cc_final: 0.8115 (mt) outliers start: 38 outliers final: 26 residues processed: 387 average time/residue: 0.3393 time to fit residues: 176.1683 Evaluate side-chains 380 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 350 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 101 LYS 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 483 ILE Chi-restraints excluded: chain C residue 499 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 711 LYS Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 244 THR 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 491 LEU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 760 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 159 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 ASN D 130 GLN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS A 547 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.138201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116836 restraints weight = 19738.616| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.18 r_work: 0.3285 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 13964 Z= 0.225 Angle : 0.555 8.939 18856 Z= 0.278 Chirality : 0.043 0.144 2060 Planarity : 0.004 0.039 2442 Dihedral : 4.043 18.573 1846 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.00 % Allowed : 21.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1648 helix: 0.50 (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 TRP 0.004 0.001 TRP B 139 HIS 0.004 0.001 HIS A 655 PHE 0.026 0.002 PHE A 475 TYR 0.022 0.002 TYR A 556 ARG 0.005 0.000 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.04639 ( 624) hydrogen bonds : angle 4.15472 ( 1740) metal coordination : bond 0.00908 ( 16) metal coordination : angle 3.59902 ( 24) covalent geometry : bond 0.00542 (13948) covalent geometry : angle 0.54042 (18832) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 371 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7774 (tp) cc_final: 0.7458 (tp) REVERT: D 62 ARG cc_start: 0.7890 (mtt-85) cc_final: 0.7545 (mtt90) REVERT: C 141 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7564 (ttp80) REVERT: C 268 GLU cc_start: 0.8087 (tt0) cc_final: 0.7592 (tm-30) REVERT: C 349 TYR cc_start: 0.8636 (t80) cc_final: 0.8365 (t80) REVERT: C 426 ASP cc_start: 0.7655 (t0) cc_final: 0.7340 (t70) REVERT: C 456 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8039 (mm-30) REVERT: C 457 VAL cc_start: 0.8717 (m) cc_final: 0.8305 (p) REVERT: C 459 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7145 (mm-30) REVERT: C 524 ARG cc_start: 0.8524 (mmm-85) cc_final: 0.8202 (mtt90) REVERT: C 539 ARG cc_start: 0.7898 (mmm160) cc_final: 0.7649 (mmm160) REVERT: C 552 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7982 (mttm) REVERT: C 595 SER cc_start: 0.8726 (t) cc_final: 0.8409 (p) REVERT: C 677 MET cc_start: 0.6832 (mmm) cc_final: 0.6629 (mmm) REVERT: C 699 ASN cc_start: 0.7488 (p0) cc_final: 0.7110 (p0) REVERT: C 719 ASP cc_start: 0.8205 (t70) cc_final: 0.7848 (t0) REVERT: C 728 LYS cc_start: 0.8345 (mtmt) cc_final: 0.8079 (mmmm) REVERT: C 793 ILE cc_start: 0.8548 (mt) cc_final: 0.8234 (mt) REVERT: B 19 LEU cc_start: 0.7918 (tp) cc_final: 0.7567 (tp) REVERT: B 28 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7646 (p) REVERT: B 93 THR cc_start: 0.7705 (OUTLIER) cc_final: 0.7324 (p) REVERT: A 235 ASP cc_start: 0.7524 (p0) cc_final: 0.6951 (p0) REVERT: A 268 GLU cc_start: 0.8028 (tt0) cc_final: 0.7388 (tm-30) REVERT: A 300 GLU cc_start: 0.8192 (pt0) cc_final: 0.7969 (pt0) REVERT: A 426 ASP cc_start: 0.7561 (t0) cc_final: 0.7243 (t70) REVERT: A 429 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7080 (mt-10) REVERT: A 456 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7943 (mm-30) REVERT: A 457 VAL cc_start: 0.8651 (m) cc_final: 0.8223 (p) REVERT: A 459 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7094 (mm-30) REVERT: A 589 MET cc_start: 0.8306 (mtm) cc_final: 0.8091 (mtm) REVERT: A 595 SER cc_start: 0.8552 (t) cc_final: 0.8226 (p) REVERT: A 635 MET cc_start: 0.8497 (tpp) cc_final: 0.8238 (tpp) REVERT: A 653 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7599 (p0) REVERT: A 667 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 712 GLU cc_start: 0.7888 (tt0) cc_final: 0.7584 (tt0) REVERT: A 728 LYS cc_start: 0.8320 (mtmt) cc_final: 0.8055 (mmmm) REVERT: A 793 ILE cc_start: 0.8540 (mt) cc_final: 0.8266 (mt) outliers start: 46 outliers final: 30 residues processed: 398 average time/residue: 0.3435 time to fit residues: 183.2071 Evaluate side-chains 398 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 364 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain C residue 137 LEU 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 483 ILE Chi-restraints excluded: chain C residue 499 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 711 LYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain B residue 28 THR 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 111 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 339 MET 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 491 LEU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 743 GLU 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 42 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 chunk 66 optimal weight: 0.0570 chunk 115 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 B 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118136 restraints weight = 19691.075| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.20 r_work: 0.3309 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2592 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= 0.102 Angle : 0.494 8.151 18856 Z= 0.247 Chirality : 0.039 0.125 2060 Planarity : 0.003 0.036 2442 Dihedral : 3.775 16.186 1846 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.96 % Allowed : 22.06 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1648 helix: 0.86 (0.18), residues: 894 sheet: -0.80 (0.67), residues: 68 loop : 0.08 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 328 HIS 0.002 0.000 HIS C 655 PHE 0.020 0.001 PHE A 475 TYR 0.015 0.001 TYR A 694 ARG 0.008 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 624) hydrogen bonds : angle 3.91721 ( 1740) metal coordination : bond 0.00312 ( 16) metal coordination : angle 2.83677 ( 24) covalent geometry : bond 0.00234 (13948) covalent geometry : angle 0.48336 (18832) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 355 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: D 124 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7702 (ttp-110) REVERT: C 141 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7568 (ttp80) REVERT: C 165 GLN cc_start: 0.8394 (mp10) cc_final: 0.7986 (mp10) REVERT: C 241 ARG cc_start: 0.8001 (ptp90) cc_final: 0.7700 (mtm110) REVERT: C 268 GLU cc_start: 0.8125 (tt0) cc_final: 0.7596 (tm-30) REVERT: C 349 TYR cc_start: 0.8626 (t80) cc_final: 0.8368 (t80) REVERT: C 426 ASP cc_start: 0.7573 (t0) cc_final: 0.7263 (t70) REVERT: C 456 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7996 (mm-30) REVERT: C 457 VAL cc_start: 0.8696 (m) cc_final: 0.8295 (p) REVERT: C 459 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7100 (mm-30) REVERT: C 541 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7726 (mm-30) REVERT: C 552 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7968 (mttp) REVERT: C 595 SER cc_start: 0.8684 (t) cc_final: 0.8369 (p) REVERT: C 677 MET cc_start: 0.6699 (mmm) cc_final: 0.6436 (mmm) REVERT: C 699 ASN cc_start: 0.7406 (p0) cc_final: 0.7037 (p0) REVERT: C 719 ASP cc_start: 0.8159 (t70) cc_final: 0.7798 (t0) REVERT: C 772 GLU cc_start: 0.8044 (tp30) cc_final: 0.7622 (tp30) REVERT: C 793 ILE cc_start: 0.8504 (mt) cc_final: 0.8158 (mt) REVERT: B 19 LEU cc_start: 0.7847 (tp) cc_final: 0.7592 (tp) REVERT: A 235 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.6910 (p0) REVERT: A 268 GLU cc_start: 0.7977 (tt0) cc_final: 0.7445 (tm-30) REVERT: A 291 MET cc_start: 0.7721 (mmm) cc_final: 0.7447 (mmm) REVERT: A 300 GLU cc_start: 0.8169 (pt0) cc_final: 0.7959 (pt0) REVERT: A 349 TYR cc_start: 0.8370 (t80) cc_final: 0.8064 (t80) REVERT: A 426 ASP cc_start: 0.7546 (t0) cc_final: 0.7218 (t70) REVERT: A 429 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7180 (tt0) REVERT: A 456 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7926 (mm-30) REVERT: A 457 VAL cc_start: 0.8660 (m) cc_final: 0.8239 (p) REVERT: A 459 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7054 (mm-30) REVERT: A 526 LYS cc_start: 0.8626 (ttpp) cc_final: 0.8424 (ttpp) REVERT: A 552 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8129 (mttp) REVERT: A 589 MET cc_start: 0.8272 (mtm) cc_final: 0.8054 (mtm) REVERT: A 595 SER cc_start: 0.8522 (t) cc_final: 0.8208 (p) REVERT: A 667 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7717 (mt-10) REVERT: A 712 GLU cc_start: 0.7848 (tt0) cc_final: 0.7533 (tt0) REVERT: A 728 LYS cc_start: 0.8310 (mtmt) cc_final: 0.8043 (mmmm) REVERT: A 742 ASN cc_start: 0.7919 (p0) cc_final: 0.6985 (p0) REVERT: A 743 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: A 782 ARG cc_start: 0.7301 (ttt90) cc_final: 0.7084 (ttt90) REVERT: A 793 ILE cc_start: 0.8516 (mt) cc_final: 0.8217 (mt) outliers start: 30 outliers final: 18 residues processed: 369 average time/residue: 0.3607 time to fit residues: 177.6902 Evaluate side-chains 374 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 352 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 311 LYS Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 483 ILE 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 C residue 760 CYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 743 GLU 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 3 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 A 684 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.137966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116553 restraints weight = 19649.347| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.19 r_work: 0.3315 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13964 Z= 0.193 Angle : 0.545 9.997 18856 Z= 0.272 Chirality : 0.042 0.137 2060 Planarity : 0.004 0.037 2442 Dihedral : 3.940 17.869 1846 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.68 % Allowed : 21.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1648 helix: 0.69 (0.18), residues: 904 sheet: -0.83 (0.67), residues: 68 loop : -0.09 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 139 HIS 0.003 0.001 HIS A 655 PHE 0.026 0.002 PHE C 475 TYR 0.017 0.002 TYR A 556 ARG 0.009 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 624) hydrogen bonds : angle 4.05703 ( 1740) metal coordination : bond 0.00757 ( 16) metal coordination : angle 3.26290 ( 24) covalent geometry : bond 0.00467 (13948) covalent geometry : angle 0.53265 (18832) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 364 time to evaluate : 1.434 Fit side-chains revert: symmetry clash REVERT: D 62 ARG cc_start: 0.7900 (mtt-85) cc_final: 0.7448 (mtt90) REVERT: D 124 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7731 (ttp-110) REVERT: C 130 GLU cc_start: 0.7557 (tt0) cc_final: 0.6329 (tt0) REVERT: C 134 TYR cc_start: 0.7764 (m-80) cc_final: 0.6880 (m-80) REVERT: C 135 GLU cc_start: 0.7765 (pp20) cc_final: 0.7558 (pp20) REVERT: C 141 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7593 (ttp80) REVERT: C 268 GLU cc_start: 0.8101 (tt0) cc_final: 0.7595 (tm-30) REVERT: C 349 TYR cc_start: 0.8618 (t80) cc_final: 0.8373 (t80) REVERT: C 426 ASP cc_start: 0.7570 (t0) cc_final: 0.7269 (t70) REVERT: C 435 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8233 (mtmt) REVERT: C 456 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8024 (mm-30) REVERT: C 457 VAL cc_start: 0.8704 (m) cc_final: 0.8297 (p) REVERT: C 459 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7108 (mm-30) REVERT: C 541 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7637 (mm-30) REVERT: C 552 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7939 (mttp) REVERT: C 595 SER cc_start: 0.8725 (t) cc_final: 0.8409 (p) REVERT: C 677 MET cc_start: 0.6802 (mmm) cc_final: 0.6458 (mmm) REVERT: C 699 ASN cc_start: 0.7502 (p0) cc_final: 0.7098 (p0) REVERT: C 719 ASP cc_start: 0.8169 (t70) cc_final: 0.7828 (t0) REVERT: C 772 GLU cc_start: 0.8024 (tp30) cc_final: 0.7595 (tp30) REVERT: C 793 ILE cc_start: 0.8538 (mt) cc_final: 0.8185 (mt) REVERT: B 19 LEU cc_start: 0.7887 (tp) cc_final: 0.7594 (tp) REVERT: B 28 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7571 (t) REVERT: B 93 THR cc_start: 0.7677 (OUTLIER) cc_final: 0.7297 (p) REVERT: B 99 TYR cc_start: 0.8296 (m-80) cc_final: 0.7481 (m-80) REVERT: B 124 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7808 (ttp-110) REVERT: A 140 CYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7399 (t) REVERT: A 235 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.6982 (p0) REVERT: A 268 GLU cc_start: 0.7954 (tt0) cc_final: 0.7442 (tm-30) REVERT: A 291 MET cc_start: 0.7718 (mmm) cc_final: 0.7422 (mmm) REVERT: A 300 GLU cc_start: 0.8175 (pt0) cc_final: 0.7956 (pt0) REVERT: A 426 ASP cc_start: 0.7497 (t0) cc_final: 0.7192 (t70) REVERT: A 429 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7158 (mt-10) REVERT: A 456 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7933 (mm-30) REVERT: A 457 VAL cc_start: 0.8649 (m) cc_final: 0.8231 (p) REVERT: A 459 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7093 (mm-30) REVERT: A 552 LYS cc_start: 0.8305 (mmtm) cc_final: 0.7972 (mttp) REVERT: A 589 MET cc_start: 0.8308 (mtm) cc_final: 0.8092 (mtm) REVERT: A 595 SER cc_start: 0.8539 (t) cc_final: 0.8209 (p) REVERT: A 667 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7744 (mt-10) REVERT: A 712 GLU cc_start: 0.7867 (tt0) cc_final: 0.7552 (tt0) REVERT: A 728 LYS cc_start: 0.8292 (mtmt) cc_final: 0.8047 (mtpp) REVERT: A 743 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: A 793 ILE cc_start: 0.8506 (mt) cc_final: 0.8238 (mt) outliers start: 41 outliers final: 25 residues processed: 386 average time/residue: 0.3378 time to fit residues: 174.0189 Evaluate side-chains 393 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 360 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 339 MET 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 724 LYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 49 VAL 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 140 CYS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 318 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 743 GLU 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 35 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 145 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 43 optimal weight: 0.0050 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118531 restraints weight = 19528.566| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.18 r_work: 0.3299 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13964 Z= 0.131 Angle : 0.513 11.003 18856 Z= 0.255 Chirality : 0.040 0.144 2060 Planarity : 0.003 0.037 2442 Dihedral : 3.808 16.630 1846 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.22 % Allowed : 22.06 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1648 helix: 0.89 (0.18), residues: 892 sheet: -0.83 (0.67), residues: 68 loop : 0.06 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 328 HIS 0.002 0.001 HIS A 655 PHE 0.023 0.001 PHE C 475 TYR 0.018 0.001 TYR A 349 ARG 0.008 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 624) hydrogen bonds : angle 3.94768 ( 1740) metal coordination : bond 0.00434 ( 16) metal coordination : angle 2.87730 ( 24) covalent geometry : bond 0.00312 (13948) covalent geometry : angle 0.50273 (18832) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 357 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 28 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7557 (t) REVERT: D 62 ARG cc_start: 0.7928 (mtt-85) cc_final: 0.7689 (mtt90) REVERT: D 124 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7748 (ttp-110) REVERT: C 130 GLU cc_start: 0.7547 (tt0) cc_final: 0.6255 (tt0) REVERT: C 134 TYR cc_start: 0.7787 (m-80) cc_final: 0.6934 (m-80) REVERT: C 138 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7150 (tp30) REVERT: C 141 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7527 (ttp80) REVERT: C 268 GLU cc_start: 0.8107 (tt0) cc_final: 0.7597 (tm-30) REVERT: C 349 TYR cc_start: 0.8598 (t80) cc_final: 0.8379 (t80) REVERT: C 426 ASP cc_start: 0.7549 (t0) cc_final: 0.7250 (t70) REVERT: C 435 LYS cc_start: 0.8492 (mtmm) cc_final: 0.8218 (mtmt) REVERT: C 456 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8010 (mm-30) REVERT: C 457 VAL cc_start: 0.8702 (m) cc_final: 0.8300 (p) REVERT: C 459 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7095 (mm-30) REVERT: C 541 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7647 (mm-30) REVERT: C 552 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7940 (mttp) REVERT: C 595 SER cc_start: 0.8692 (t) cc_final: 0.8369 (p) REVERT: C 677 MET cc_start: 0.6772 (mmm) cc_final: 0.6411 (mmm) REVERT: C 699 ASN cc_start: 0.7481 (p0) cc_final: 0.7075 (p0) REVERT: C 719 ASP cc_start: 0.8140 (t70) cc_final: 0.7796 (t0) REVERT: C 743 GLU cc_start: 0.7659 (mp0) cc_final: 0.7334 (mp0) REVERT: C 772 GLU cc_start: 0.8044 (tp30) cc_final: 0.7632 (tp30) REVERT: C 793 ILE cc_start: 0.8533 (mt) cc_final: 0.8177 (mt) REVERT: B 19 LEU cc_start: 0.7862 (tp) cc_final: 0.7585 (tp) REVERT: B 93 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7274 (p) REVERT: B 99 TYR cc_start: 0.8290 (m-80) cc_final: 0.7493 (m-80) REVERT: B 124 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7820 (ttp-110) REVERT: A 134 TYR cc_start: 0.7879 (m-10) cc_final: 0.7665 (m-10) REVERT: A 140 CYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7407 (t) REVERT: A 235 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6935 (p0) REVERT: A 268 GLU cc_start: 0.7931 (tt0) cc_final: 0.7451 (tm-30) REVERT: A 291 MET cc_start: 0.7663 (mmm) cc_final: 0.7381 (mmm) REVERT: A 300 GLU cc_start: 0.8167 (pt0) cc_final: 0.7941 (pt0) REVERT: A 426 ASP cc_start: 0.7506 (t0) cc_final: 0.7187 (t70) REVERT: A 429 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7178 (tt0) REVERT: A 456 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7947 (mm-30) REVERT: A 457 VAL cc_start: 0.8666 (m) cc_final: 0.8332 (p) REVERT: A 459 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7019 (mm-30) REVERT: A 552 LYS cc_start: 0.8340 (mmtm) cc_final: 0.7994 (mttp) REVERT: A 589 MET cc_start: 0.8278 (mtm) cc_final: 0.8060 (mtm) REVERT: A 595 SER cc_start: 0.8521 (t) cc_final: 0.8205 (p) REVERT: A 667 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7746 (mt-10) REVERT: A 712 GLU cc_start: 0.7829 (tt0) cc_final: 0.7522 (tt0) REVERT: A 728 LYS cc_start: 0.8255 (mtmt) cc_final: 0.8005 (mmmm) REVERT: A 742 ASN cc_start: 0.7899 (p0) cc_final: 0.6990 (p0) REVERT: A 743 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: A 793 ILE cc_start: 0.8499 (mt) cc_final: 0.8211 (mt) outliers start: 34 outliers final: 23 residues processed: 377 average time/residue: 0.3547 time to fit residues: 177.9203 Evaluate side-chains 385 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 354 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 49 VAL 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 311 LYS 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 B residue 49 VAL 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 235 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 318 LEU 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 743 GLU 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 108 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 126 optimal weight: 0.0980 chunk 38 optimal weight: 0.4980 chunk 54 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.139844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118739 restraints weight = 19505.613| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.17 r_work: 0.3320 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13964 Z= 0.108 Angle : 0.500 11.768 18856 Z= 0.249 Chirality : 0.039 0.135 2060 Planarity : 0.003 0.037 2442 Dihedral : 3.677 15.645 1846 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.89 % Allowed : 22.39 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1648 helix: 1.06 (0.18), residues: 898 sheet: -0.84 (0.66), residues: 68 loop : 0.07 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 600 HIS 0.002 0.000 HIS A 655 PHE 0.023 0.001 PHE C 475 TYR 0.017 0.001 TYR A 349 ARG 0.009 0.000 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 624) hydrogen bonds : angle 3.84981 ( 1740) metal coordination : bond 0.00305 ( 16) metal coordination : angle 2.80409 ( 24) covalent geometry : bond 0.00253 (13948) covalent geometry : angle 0.49039 (18832) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 353 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 28 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7578 (t) REVERT: D 99 TYR cc_start: 0.8033 (m-80) cc_final: 0.7382 (m-80) REVERT: D 124 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7647 (ttp-110) REVERT: C 130 GLU cc_start: 0.7502 (tt0) cc_final: 0.6223 (tt0) REVERT: C 134 TYR cc_start: 0.7771 (m-80) cc_final: 0.6913 (m-80) REVERT: C 141 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7502 (ttp80) REVERT: C 165 GLN cc_start: 0.8372 (mp10) cc_final: 0.7952 (mp10) REVERT: C 268 GLU cc_start: 0.8075 (tt0) cc_final: 0.7583 (tm-30) REVERT: C 349 TYR cc_start: 0.8534 (t80) cc_final: 0.8315 (t80) REVERT: C 426 ASP cc_start: 0.7534 (t0) cc_final: 0.7219 (t70) REVERT: C 435 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8188 (mtmt) REVERT: C 456 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7972 (mm-30) REVERT: C 457 VAL cc_start: 0.8695 (m) cc_final: 0.8283 (p) REVERT: C 459 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7067 (mm-30) REVERT: C 541 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7576 (mm-30) REVERT: C 552 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7952 (mttp) REVERT: C 595 SER cc_start: 0.8664 (t) cc_final: 0.8344 (p) REVERT: C 654 SER cc_start: 0.8018 (t) cc_final: 0.7772 (t) REVERT: C 677 MET cc_start: 0.6739 (mmm) cc_final: 0.6516 (mmm) REVERT: C 699 ASN cc_start: 0.7453 (p0) cc_final: 0.7053 (p0) REVERT: C 719 ASP cc_start: 0.8092 (t70) cc_final: 0.7742 (t0) REVERT: C 793 ILE cc_start: 0.8460 (mt) cc_final: 0.8107 (mt) REVERT: B 19 LEU cc_start: 0.7821 (tp) cc_final: 0.7540 (tp) REVERT: B 99 TYR cc_start: 0.8271 (m-80) cc_final: 0.7530 (m-80) REVERT: B 124 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7763 (ttp-110) REVERT: A 134 TYR cc_start: 0.7890 (m-10) cc_final: 0.7669 (m-10) REVERT: A 140 CYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7372 (t) REVERT: A 235 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.6800 (p0) REVERT: A 268 GLU cc_start: 0.7899 (tt0) cc_final: 0.7480 (tm-30) REVERT: A 291 MET cc_start: 0.7610 (mmm) cc_final: 0.7330 (mmm) REVERT: A 300 GLU cc_start: 0.8128 (pt0) cc_final: 0.7899 (pt0) REVERT: A 313 MET cc_start: 0.8528 (ttp) cc_final: 0.8262 (ttp) REVERT: A 426 ASP cc_start: 0.7492 (t0) cc_final: 0.7176 (t70) REVERT: A 429 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7169 (tt0) REVERT: A 456 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7890 (mm-30) REVERT: A 457 VAL cc_start: 0.8641 (m) cc_final: 0.8307 (p) REVERT: A 459 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6972 (mm-30) REVERT: A 552 LYS cc_start: 0.8393 (mmtm) cc_final: 0.7988 (mttp) REVERT: A 595 SER cc_start: 0.8504 (t) cc_final: 0.8189 (p) REVERT: A 667 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 712 GLU cc_start: 0.7794 (tt0) cc_final: 0.7474 (tt0) REVERT: A 728 LYS cc_start: 0.8289 (mtmt) cc_final: 0.8042 (mtpp) REVERT: A 743 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: A 782 ARG cc_start: 0.7266 (ttt90) cc_final: 0.7045 (ttt90) REVERT: A 793 ILE cc_start: 0.8468 (mt) cc_final: 0.8162 (mt) outliers start: 29 outliers final: 21 residues processed: 371 average time/residue: 0.3583 time to fit residues: 176.4581 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 : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR 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 311 LYS Chi-restraints excluded: chain C residue 327 LEU 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 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 235 ASP Chi-restraints excluded: chain A residue 318 LEU 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 743 GLU 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 58 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 136 optimal weight: 0.0060 chunk 98 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN 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 = 0.139412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118195 restraints weight = 19695.906| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.19 r_work: 0.3334 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2801 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= 0.128 Angle : 0.520 11.735 18856 Z= 0.258 Chirality : 0.040 0.138 2060 Planarity : 0.003 0.037 2442 Dihedral : 3.700 15.458 1846 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.09 % Allowed : 22.78 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1648 helix: 1.06 (0.18), residues: 898 sheet: -0.90 (0.66), residues: 68 loop : 0.05 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 600 HIS 0.002 0.001 HIS A 655 PHE 0.026 0.001 PHE A 475 TYR 0.021 0.001 TYR A 668 ARG 0.008 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 624) hydrogen bonds : angle 3.88628 ( 1740) metal coordination : bond 0.00413 ( 16) metal coordination : angle 2.81529 ( 24) covalent geometry : bond 0.00307 (13948) covalent geometry : angle 0.51055 (18832) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8731.38 seconds wall clock time: 149 minutes 31.32 seconds (8971.32 seconds total)