Starting phenix.real_space_refine on Wed Mar 4 19:02:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzi_24761/03_2026/7rzi_24761.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzi_24761/03_2026/7rzi_24761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rzi_24761/03_2026/7rzi_24761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzi_24761/03_2026/7rzi_24761.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzi_24761/03_2026/7rzi_24761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzi_24761/03_2026/7rzi_24761.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 10134 2.51 5 N 2640 2.21 5 O 2913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15736 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7763 Classifications: {'peptide': 948} Link IDs: {'PTRANS': 51, 'TRANS': 896} Chain breaks: 1 Chain: "B" Number of atoms: 7692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7692 Classifications: {'peptide': 938} Link IDs: {'PTRANS': 48, 'TRANS': 889} Chain breaks: 1 Chain: "a" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 83 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "b" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "c" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 108 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "d" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Time building chain proxies: 3.53, per 1000 atoms: 0.22 Number of scatterers: 15736 At special positions: 0 Unit cell: (108.42, 131.188, 149.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 2913 8.00 N 2640 7.00 C 10134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS a 6 " - pdb=" SG CYS a 11 " distance=1.74 Simple disulfide: pdb=" SG CYS c 6 " - pdb=" SG CYS c 11 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 575.7 milliseconds 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3666 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 10 sheets defined 45.0% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.571A pdb=" N SER A 98 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 99' Processing helix chain 'A' and resid 105 through 115 removed outlier: 4.164A pdb=" N PHE A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 158 through 171 removed outlier: 4.298A pdb=" N ARG A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 193 removed outlier: 4.275A pdb=" N VAL A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 removed outlier: 3.627A pdb=" N LEU A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 237 through 249 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.545A pdb=" N LEU A 298 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 345 through 353 removed outlier: 3.645A pdb=" N LEU A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 405 removed outlier: 3.701A pdb=" N GLU A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.689A pdb=" N PHE A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 440 removed outlier: 3.520A pdb=" N TYR A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER A 435 " --> pdb=" O ARG A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.863A pdb=" N ILE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 removed outlier: 3.982A pdb=" N ILE A 510 " --> pdb=" O PRO A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 615 removed outlier: 3.821A pdb=" N ALA A 593 " --> pdb=" O HIS A 589 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TYR A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ALA A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 removed outlier: 3.589A pdb=" N LEU A 641 " --> pdb=" O LYS A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.826A pdb=" N GLU A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 671 " --> pdb=" O MET A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 677 through 690 removed outlier: 3.861A pdb=" N ARG A 687 " --> pdb=" O MET A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 removed outlier: 3.787A pdb=" N LEU A 700 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 696 through 701' Processing helix chain 'A' and resid 708 through 720 removed outlier: 3.538A pdb=" N ILE A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) Proline residue: A 717 - end of helix Processing helix chain 'A' and resid 734 through 754 Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.684A pdb=" N LEU A 763 " --> pdb=" O PRO A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 3.942A pdb=" N LEU A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 824 removed outlier: 3.884A pdb=" N PHE A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 877 removed outlier: 3.516A pdb=" N LEU A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 877 " --> pdb=" O SER A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 894 Processing helix chain 'A' and resid 900 through 912 removed outlier: 3.757A pdb=" N LYS A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU A 910 " --> pdb=" O LYS A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 929 Processing helix chain 'A' and resid 932 through 944 removed outlier: 3.892A pdb=" N ILE A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1001 removed outlier: 4.116A pdb=" N GLY A1001 " --> pdb=" O GLU A 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 removed outlier: 4.241A pdb=" N PHE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 removed outlier: 3.697A pdb=" N GLU B 133 " --> pdb=" O GLN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 166 removed outlier: 4.301A pdb=" N ASP B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.885A pdb=" N SER B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 181 through 192 removed outlier: 3.593A pdb=" N ALA B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 207 removed outlier: 3.831A pdb=" N PHE B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 264 through 276 removed outlier: 3.511A pdb=" N THR B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU B 270 " --> pdb=" O ASP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 removed outlier: 3.541A pdb=" N TYR B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 removed outlier: 3.660A pdb=" N LYS B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 408 through 424 removed outlier: 3.533A pdb=" N ASN B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 440 removed outlier: 3.529A pdb=" N THR B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N SER B 435 " --> pdb=" O ARG B 431 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 437 " --> pdb=" O TYR B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 443 No H-bonds generated for 'chain 'B' and resid 441 through 443' Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.767A pdb=" N ILE B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.748A pdb=" N VAL B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 Processing helix chain 'B' and resid 506 through 514 removed outlier: 3.589A pdb=" N ILE B 510 " --> pdb=" O PRO B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 604 through 613 removed outlier: 5.087A pdb=" N ALA B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 613 " --> pdb=" O TYR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 650 removed outlier: 3.590A pdb=" N LEU B 641 " --> pdb=" O LYS B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 677 through 691 removed outlier: 3.622A pdb=" N HIS B 681 " --> pdb=" O GLN B 677 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B 682 " --> pdb=" O PRO B 678 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET B 683 " --> pdb=" O HIS B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 708 through 714 removed outlier: 3.786A pdb=" N ALA B 714 " --> pdb=" O PRO B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 720 removed outlier: 3.507A pdb=" N GLN B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 754 removed outlier: 3.796A pdb=" N LEU B 739 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 745 " --> pdb=" O ILE B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.659A pdb=" N LEU B 763 " --> pdb=" O PRO B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 815 removed outlier: 3.674A pdb=" N MET B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 807 " --> pdb=" O SER B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 855 through 876 removed outlier: 4.170A pdb=" N SER B 861 " --> pdb=" O HIS B 857 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 862 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 863 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP B 876 " --> pdb=" O LYS B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 893 removed outlier: 3.714A pdb=" N LEU B 889 " --> pdb=" O HIS B 885 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 890 " --> pdb=" O ILE B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 912 removed outlier: 3.590A pdb=" N GLU B 903 " --> pdb=" O LYS B 899 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY B 909 " --> pdb=" O ALA B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 929 removed outlier: 3.538A pdb=" N THR B 923 " --> pdb=" O ASP B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 944 removed outlier: 3.575A pdb=" N ILE B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1001 removed outlier: 4.003A pdb=" N GLY B1001 " --> pdb=" O GLU B 997 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.016A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 88 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 142 " --> pdb=" O SER a 12 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER a 12 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 360 removed outlier: 4.878A pdb=" N THR A 358 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ARG A 311 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 491 through 492 Processing sheet with id=AA4, first strand: chain 'A' and resid 557 through 558 removed outlier: 6.416A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 724 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 728 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 575 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 563 Processing sheet with id=AA6, first strand: chain 'A' and resid 832 through 840 removed outlier: 4.540A pdb=" N ILE A 832 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 851 " --> pdb=" O ILE A 832 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN A 844 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N HIS A 952 " --> pdb=" O GLN A 796 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP A 776 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.646A pdb=" N GLU B 63 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS B 74 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL B 258 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B 76 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLY B 260 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE B 78 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 88 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 141 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 356 through 367 removed outlier: 4.594A pdb=" N THR B 358 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 366 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLN B 499 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 549 through 553 removed outlier: 6.331A pdb=" N LEU B 550 " --> pdb=" O PHE B 561 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE B 561 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS B 552 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS B 558 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU B 729 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N TRP B 560 " --> pdb=" O LEU B 729 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 775 through 782 removed outlier: 5.918A pdb=" N GLY B 775 " --> pdb=" O LYS B 953 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER B 955 " --> pdb=" O GLY B 775 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR B 779 " --> pdb=" O HIS B 957 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU B 959 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU B 792 " --> pdb=" O VAL B 956 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 850 " --> pdb=" O ILE B 791 " (cutoff:3.500A) 661 hydrogen bonds defined for protein. 1902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3459 1.33 - 1.45: 3547 1.45 - 1.57: 9025 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 16123 Sorted by residual: bond pdb=" N GLY B 366 " pdb=" CA GLY B 366 " ideal model delta sigma weight residual 1.447 1.475 -0.028 7.50e-03 1.78e+04 1.41e+01 bond pdb=" N TYR A 766 " pdb=" CA TYR A 766 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.18e-02 7.18e+03 1.04e+01 bond pdb=" N VAL B 360 " pdb=" CA VAL B 360 " ideal model delta sigma weight residual 1.458 1.496 -0.037 1.19e-02 7.06e+03 9.89e+00 bond pdb=" N VAL B 764 " pdb=" CA VAL B 764 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.32e-02 5.74e+03 9.59e+00 bond pdb=" N ILE B 103 " pdb=" CA ILE B 103 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.37e+00 ... (remaining 16118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 20622 2.05 - 4.10: 1042 4.10 - 6.16: 105 6.16 - 8.21: 19 8.21 - 10.26: 9 Bond angle restraints: 21797 Sorted by residual: angle pdb=" N LEU B 763 " pdb=" CA LEU B 763 " pdb=" C LEU B 763 " ideal model delta sigma weight residual 112.25 105.14 7.11 1.36e+00 5.41e-01 2.73e+01 angle pdb=" N ILE a 10 " pdb=" CA ILE a 10 " pdb=" C ILE a 10 " ideal model delta sigma weight residual 112.90 108.05 4.85 9.60e-01 1.09e+00 2.55e+01 angle pdb=" O GLY B 366 " pdb=" C GLY B 366 " pdb=" N ALA B 367 " ideal model delta sigma weight residual 121.85 124.41 -2.56 5.60e-01 3.19e+00 2.08e+01 angle pdb=" N GLN B 796 " pdb=" CA GLN B 796 " pdb=" C GLN B 796 " ideal model delta sigma weight residual 111.71 116.36 -4.65 1.15e+00 7.56e-01 1.64e+01 angle pdb=" CA GLU A 277 " pdb=" C GLU A 277 " pdb=" O GLU A 277 " ideal model delta sigma weight residual 121.00 116.86 4.14 1.05e+00 9.07e-01 1.56e+01 ... (remaining 21792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 8954 16.92 - 33.83: 654 33.83 - 50.75: 126 50.75 - 67.67: 18 67.67 - 84.58: 11 Dihedral angle restraints: 9763 sinusoidal: 4096 harmonic: 5667 Sorted by residual: dihedral pdb=" CB CYS c 6 " pdb=" SG CYS c 6 " pdb=" SG CYS c 11 " pdb=" CB CYS c 11 " ideal model delta sinusoidal sigma weight residual -86.00 -136.67 50.67 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CA LYS A 511 " pdb=" C LYS A 511 " pdb=" N LYS A 512 " pdb=" CA LYS A 512 " ideal model delta harmonic sigma weight residual 180.00 153.46 26.54 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA ARG A 261 " pdb=" C ARG A 261 " pdb=" N GLU A 262 " pdb=" CA GLU A 262 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 9760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1891 0.074 - 0.147: 399 0.147 - 0.221: 46 0.221 - 0.294: 7 0.294 - 0.368: 2 Chirality restraints: 2345 Sorted by residual: chirality pdb=" CA THR B 797 " pdb=" N THR B 797 " pdb=" C THR B 797 " pdb=" CB THR B 797 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA GLN B 796 " pdb=" N GLN B 796 " pdb=" C GLN B 796 " pdb=" CB GLN B 796 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA MET A 742 " pdb=" N MET A 742 " pdb=" C MET A 742 " pdb=" CB MET A 742 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2342 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 821 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C ASN B 821 " 0.069 2.00e-02 2.50e+03 pdb=" O ASN B 821 " -0.026 2.00e-02 2.50e+03 pdb=" N THR B 822 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 224 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C TYR A 224 " -0.063 2.00e-02 2.50e+03 pdb=" O TYR A 224 " 0.024 2.00e-02 2.50e+03 pdb=" N THR A 225 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 223 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C LYS A 223 " 0.056 2.00e-02 2.50e+03 pdb=" O LYS A 223 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR A 224 " -0.019 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1529 2.74 - 3.28: 15138 3.28 - 3.82: 24813 3.82 - 4.36: 31533 4.36 - 4.90: 53395 Nonbonded interactions: 126408 Sorted by model distance: nonbonded pdb=" OG SER A 87 " pdb=" O PHE A 151 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG B 402 " pdb=" O LEU B 471 " model vdw 2.209 3.120 nonbonded pdb=" O MET A 877 " pdb=" NZ LYS A 933 " model vdw 2.231 3.120 nonbonded pdb=" OG1 THR A 623 " pdb=" O GLY A 626 " model vdw 2.236 3.040 nonbonded pdb=" O TYR A 634 " pdb=" NE2 GLN A 638 " model vdw 2.248 3.120 ... (remaining 126403 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 47 through 962 or resid 990 through 1011)) selection = chain 'B' } ncs_group { reference = chain 'b' selection = chain 'd' } 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.210 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 : 0.006 0.290 16125 Z= 0.357 Angle : 0.988 23.191 21801 Z= 0.587 Chirality : 0.060 0.368 2345 Planarity : 0.008 0.079 2818 Dihedral : 12.553 84.585 6091 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.47 % Allowed : 2.50 % Favored : 97.03 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.04 (0.15), residues: 1905 helix: -3.20 (0.13), residues: 759 sheet: -1.85 (0.26), residues: 347 loop : -2.32 (0.18), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 261 TYR 0.029 0.003 TYR A 940 PHE 0.042 0.003 PHE A 168 TRP 0.034 0.003 TRP A 695 HIS 0.017 0.002 HIS B 291 Details of bonding type rmsd covalent geometry : bond 0.00573 (16123) covalent geometry : angle 0.97152 (21797) SS BOND : bond 0.20524 ( 2) SS BOND : angle 13.13782 ( 4) hydrogen bonds : bond 0.19937 ( 661) hydrogen bonds : angle 8.36895 ( 1902) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 308 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 195 MET cc_start: 0.8893 (mmt) cc_final: 0.8176 (mmt) REVERT: B 358 THR cc_start: 0.8399 (p) cc_final: 0.8153 (m) REVERT: B 526 THR cc_start: 0.8041 (p) cc_final: 0.7830 (t) REVERT: B 872 LYS cc_start: 0.7825 (mttp) cc_final: 0.7193 (tmmt) REVERT: c 5 GLN cc_start: 0.5489 (OUTLIER) cc_final: 0.4492 (mm-40) outliers start: 8 outliers final: 1 residues processed: 314 average time/residue: 0.6362 time to fit residues: 218.7922 Evaluate side-chains 188 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain c residue 5 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN A 805 ASN A 957 HIS B 93 HIS B 148 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 605 ASN B 677 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 788 ASN B 796 GLN ** B 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 HIS d 5 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.122643 restraints weight = 17127.587| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.23 r_work: 0.3273 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16125 Z= 0.203 Angle : 0.729 8.364 21801 Z= 0.370 Chirality : 0.048 0.176 2345 Planarity : 0.006 0.054 2818 Dihedral : 5.389 22.457 2088 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.61 % Allowed : 10.83 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.17), residues: 1905 helix: -1.25 (0.17), residues: 795 sheet: -1.00 (0.26), residues: 364 loop : -1.85 (0.19), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 477 TYR 0.027 0.002 TYR A 634 PHE 0.025 0.003 PHE B 918 TRP 0.023 0.002 TRP A 776 HIS 0.012 0.002 HIS B 957 Details of bonding type rmsd covalent geometry : bond 0.00495 (16123) covalent geometry : angle 0.72904 (21797) SS BOND : bond 0.00315 ( 2) SS BOND : angle 1.35361 ( 4) hydrogen bonds : bond 0.05402 ( 661) hydrogen bonds : angle 5.56471 ( 1902) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 0.558 Fit side-chains REVERT: A 146 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.5762 (p90) REVERT: A 458 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7196 (pm20) REVERT: A 543 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.6312 (pp20) REVERT: A 713 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8083 (ttpt) REVERT: A 792 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8424 (tp30) REVERT: A 872 LYS cc_start: 0.7312 (tptp) cc_final: 0.6688 (ttpp) REVERT: B 526 THR cc_start: 0.8219 (p) cc_final: 0.7881 (t) REVERT: B 774 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7053 (mtp85) REVERT: B 872 LYS cc_start: 0.7348 (mttp) cc_final: 0.6662 (tmmt) REVERT: B 997 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7220 (tt0) outliers start: 62 outliers final: 15 residues processed: 257 average time/residue: 0.6273 time to fit residues: 177.8687 Evaluate side-chains 195 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 764 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 42 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A 680 GLN A 915 GLN B 93 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN B 680 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 743 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.153858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.133892 restraints weight = 16621.373| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.22 r_work: 0.3384 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16125 Z= 0.117 Angle : 0.565 7.077 21801 Z= 0.291 Chirality : 0.043 0.149 2345 Planarity : 0.004 0.049 2818 Dihedral : 4.789 21.739 2083 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.79 % Allowed : 13.92 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.18), residues: 1905 helix: -0.27 (0.18), residues: 793 sheet: -0.48 (0.27), residues: 362 loop : -1.66 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 491 TYR 0.017 0.001 TYR A 224 PHE 0.019 0.002 PHE B 169 TRP 0.011 0.001 TRP A 776 HIS 0.007 0.001 HIS B 957 Details of bonding type rmsd covalent geometry : bond 0.00268 (16123) covalent geometry : angle 0.56425 (21797) SS BOND : bond 0.00189 ( 2) SS BOND : angle 1.39255 ( 4) hydrogen bonds : bond 0.04071 ( 661) hydrogen bonds : angle 5.02856 ( 1902) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 204 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 146 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.5653 (p90) REVERT: A 175 ASP cc_start: 0.6795 (p0) cc_final: 0.6348 (m-30) REVERT: A 205 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6651 (mp0) REVERT: A 266 ASP cc_start: 0.7442 (m-30) cc_final: 0.7172 (t70) REVERT: A 448 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7969 (pt0) REVERT: A 543 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6423 (pp20) REVERT: A 575 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8362 (p0) REVERT: A 635 ASN cc_start: 0.7543 (t0) cc_final: 0.7280 (t0) REVERT: A 699 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: A 702 GLU cc_start: 0.8380 (mp0) cc_final: 0.8016 (mp0) REVERT: A 792 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8607 (tp30) REVERT: A 813 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7487 (tp40) REVERT: A 872 LYS cc_start: 0.7398 (tptp) cc_final: 0.6771 (ttpp) REVERT: B 82 THR cc_start: 0.9048 (m) cc_final: 0.8601 (p) REVERT: B 416 ASP cc_start: 0.7609 (m-30) cc_final: 0.7396 (m-30) REVERT: B 500 TYR cc_start: 0.8526 (p90) cc_final: 0.8297 (p90) REVERT: B 521 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6531 (ptpp) REVERT: B 774 ARG cc_start: 0.8014 (mtp85) cc_final: 0.7366 (mtp85) REVERT: B 872 LYS cc_start: 0.7477 (mttp) cc_final: 0.6826 (tmmt) REVERT: B 997 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7473 (tt0) REVERT: B 1000 ARG cc_start: 0.8005 (ttm170) cc_final: 0.7700 (mtm-85) outliers start: 65 outliers final: 22 residues processed: 251 average time/residue: 0.5960 time to fit residues: 166.0904 Evaluate side-chains 215 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 813 GLN Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 956 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 166 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 0.0970 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A 680 GLN A 788 ASN B 93 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.145617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.123632 restraints weight = 16930.668| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.33 r_work: 0.3307 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16125 Z= 0.145 Angle : 0.599 7.987 21801 Z= 0.304 Chirality : 0.044 0.150 2345 Planarity : 0.004 0.049 2818 Dihedral : 4.671 20.326 2083 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.43 % Allowed : 14.50 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.19), residues: 1905 helix: 0.24 (0.19), residues: 794 sheet: -0.10 (0.28), residues: 363 loop : -1.51 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 961 TYR 0.018 0.002 TYR A 302 PHE 0.021 0.002 PHE B 169 TRP 0.010 0.001 TRP A 776 HIS 0.010 0.001 HIS B 957 Details of bonding type rmsd covalent geometry : bond 0.00351 (16123) covalent geometry : angle 0.59814 (21797) SS BOND : bond 0.00036 ( 2) SS BOND : angle 1.74799 ( 4) hydrogen bonds : bond 0.04309 ( 661) hydrogen bonds : angle 4.86689 ( 1902) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 195 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7853 (mttm) cc_final: 0.7442 (mmtt) REVERT: A 146 HIS cc_start: 0.7488 (OUTLIER) cc_final: 0.6824 (p90) REVERT: A 175 ASP cc_start: 0.6841 (p0) cc_final: 0.6469 (m-30) REVERT: A 266 ASP cc_start: 0.7504 (m-30) cc_final: 0.7085 (t70) REVERT: A 288 PHE cc_start: 0.6511 (OUTLIER) cc_final: 0.5014 (p90) REVERT: A 448 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7932 (pt0) REVERT: A 543 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6609 (pp20) REVERT: A 575 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8166 (p0) REVERT: A 699 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: A 702 GLU cc_start: 0.8435 (mp0) cc_final: 0.8224 (mp0) REVERT: A 728 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8008 (tt) REVERT: A 872 LYS cc_start: 0.7466 (tptp) cc_final: 0.6853 (ttpp) REVERT: B 159 GLU cc_start: 0.7703 (tp30) cc_final: 0.7319 (tp30) REVERT: B 205 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6834 (tp30) REVERT: B 416 ASP cc_start: 0.7603 (m-30) cc_final: 0.7347 (m-30) REVERT: B 436 LYS cc_start: 0.7676 (ttpp) cc_final: 0.7374 (mtpp) REVERT: B 500 TYR cc_start: 0.8614 (p90) cc_final: 0.8408 (p90) REVERT: B 667 MET cc_start: 0.8663 (tpp) cc_final: 0.8401 (tpt) REVERT: B 746 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7018 (pt0) REVERT: B 774 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7317 (mtp85) REVERT: B 853 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7760 (mt-10) REVERT: B 872 LYS cc_start: 0.7441 (mttp) cc_final: 0.6761 (tmmt) REVERT: B 997 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7465 (tt0) outliers start: 76 outliers final: 24 residues processed: 253 average time/residue: 0.6008 time to fit residues: 167.9834 Evaluate side-chains 214 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 956 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 130 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 186 optimal weight: 0.0970 chunk 161 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 HIS ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A 680 GLN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.147053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.125498 restraints weight = 16613.926| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.27 r_work: 0.3287 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16125 Z= 0.143 Angle : 0.582 7.676 21801 Z= 0.296 Chirality : 0.044 0.143 2345 Planarity : 0.004 0.048 2818 Dihedral : 4.618 19.269 2083 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.19 % Allowed : 15.73 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.19), residues: 1905 helix: 0.53 (0.19), residues: 796 sheet: 0.09 (0.27), residues: 363 loop : -1.43 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 229 TYR 0.019 0.002 TYR A 302 PHE 0.020 0.002 PHE B 169 TRP 0.010 0.001 TRP A 776 HIS 0.009 0.001 HIS B 957 Details of bonding type rmsd covalent geometry : bond 0.00351 (16123) covalent geometry : angle 0.57950 (21797) SS BOND : bond 0.00449 ( 2) SS BOND : angle 3.86875 ( 4) hydrogen bonds : bond 0.04212 ( 661) hydrogen bonds : angle 4.78459 ( 1902) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 195 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7845 (mttm) cc_final: 0.7338 (mmtt) REVERT: A 146 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.6831 (p90) REVERT: A 175 ASP cc_start: 0.6757 (p0) cc_final: 0.6445 (m-30) REVERT: A 180 ASP cc_start: 0.7698 (m-30) cc_final: 0.7482 (m-30) REVERT: A 227 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: A 266 ASP cc_start: 0.7304 (m-30) cc_final: 0.7078 (t70) REVERT: A 288 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.5146 (p90) REVERT: A 448 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7929 (pt0) REVERT: A 575 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8145 (p0) REVERT: A 649 MET cc_start: 0.9013 (ttp) cc_final: 0.8756 (mtp) REVERT: A 657 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7281 (mttp) REVERT: A 699 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8077 (mt-10) REVERT: A 702 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: A 728 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7966 (tt) REVERT: A 872 LYS cc_start: 0.7362 (tptp) cc_final: 0.6788 (ttpp) REVERT: B 90 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7352 (pt) REVERT: B 159 GLU cc_start: 0.7677 (tp30) cc_final: 0.7313 (tt0) REVERT: B 205 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6885 (tp30) REVERT: B 416 ASP cc_start: 0.7585 (m-30) cc_final: 0.7356 (m-30) REVERT: B 436 LYS cc_start: 0.7666 (ttpp) cc_final: 0.7371 (mtpp) REVERT: B 667 MET cc_start: 0.8591 (tpp) cc_final: 0.8305 (tpt) REVERT: B 774 ARG cc_start: 0.7995 (mtp85) cc_final: 0.7368 (mtp85) REVERT: B 853 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7752 (mt-10) REVERT: B 872 LYS cc_start: 0.7439 (mttp) cc_final: 0.6777 (tmmt) REVERT: B 997 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7311 (tt0) outliers start: 72 outliers final: 23 residues processed: 247 average time/residue: 0.6050 time to fit residues: 165.0341 Evaluate side-chains 218 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 22 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A 635 ASN A 680 GLN ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 GLN A 796 GLN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.139213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117811 restraints weight = 17046.283| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.24 r_work: 0.3216 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16125 Z= 0.184 Angle : 0.640 7.392 21801 Z= 0.324 Chirality : 0.046 0.160 2345 Planarity : 0.004 0.048 2818 Dihedral : 4.753 19.110 2083 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.14 % Allowed : 16.95 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.19), residues: 1905 helix: 0.51 (0.19), residues: 798 sheet: 0.24 (0.27), residues: 366 loop : -1.44 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 951 TYR 0.023 0.002 TYR A 302 PHE 0.023 0.002 PHE B 169 TRP 0.013 0.001 TRP A 776 HIS 0.011 0.002 HIS B 957 Details of bonding type rmsd covalent geometry : bond 0.00462 (16123) covalent geometry : angle 0.63907 (21797) SS BOND : bond 0.00456 ( 2) SS BOND : angle 3.12119 ( 4) hydrogen bonds : bond 0.04796 ( 661) hydrogen bonds : angle 4.87126 ( 1902) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 187 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7899 (mttm) cc_final: 0.7330 (mmtt) REVERT: A 146 HIS cc_start: 0.7521 (OUTLIER) cc_final: 0.6593 (p90) REVERT: A 180 ASP cc_start: 0.7740 (m-30) cc_final: 0.7536 (m-30) REVERT: A 227 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: A 266 ASP cc_start: 0.7416 (m-30) cc_final: 0.7206 (t0) REVERT: A 288 PHE cc_start: 0.6182 (OUTLIER) cc_final: 0.5921 (p90) REVERT: A 297 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.7110 (p-80) REVERT: A 448 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7883 (pt0) REVERT: A 458 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7639 (pm20) REVERT: A 543 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6498 (pp20) REVERT: A 657 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7399 (mttp) REVERT: A 702 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: A 728 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8060 (tt) REVERT: A 872 LYS cc_start: 0.7435 (tptp) cc_final: 0.6924 (ttpp) REVERT: B 90 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7549 (pt) REVERT: B 155 HIS cc_start: 0.5408 (OUTLIER) cc_final: 0.5021 (t-170) REVERT: B 159 GLU cc_start: 0.7696 (tp30) cc_final: 0.7345 (tt0) REVERT: B 163 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7223 (m-30) REVERT: B 205 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7004 (tp30) REVERT: B 381 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: B 407 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7110 (mp10) REVERT: B 416 ASP cc_start: 0.7728 (m-30) cc_final: 0.7490 (m-30) REVERT: B 436 LYS cc_start: 0.7740 (ttpp) cc_final: 0.7451 (mtpp) REVERT: B 768 GLU cc_start: 0.8517 (tt0) cc_final: 0.8297 (tt0) REVERT: B 774 ARG cc_start: 0.7995 (mtp85) cc_final: 0.7339 (mtp85) REVERT: B 853 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7757 (mt-10) REVERT: B 872 LYS cc_start: 0.7660 (mttp) cc_final: 0.6891 (tmmt) REVERT: B 997 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7365 (tt0) outliers start: 71 outliers final: 32 residues processed: 233 average time/residue: 0.6032 time to fit residues: 155.1393 Evaluate side-chains 227 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 956 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 117 optimal weight: 10.0000 chunk 99 optimal weight: 0.0870 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A 680 GLN A 796 GLN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.146221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124913 restraints weight = 16477.815| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.25 r_work: 0.3288 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16125 Z= 0.114 Angle : 0.540 6.158 21801 Z= 0.278 Chirality : 0.043 0.144 2345 Planarity : 0.004 0.045 2818 Dihedral : 4.451 18.362 2083 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.49 % Allowed : 18.35 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.19), residues: 1905 helix: 0.83 (0.19), residues: 798 sheet: 0.23 (0.28), residues: 363 loop : -1.26 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 261 TYR 0.015 0.001 TYR B 500 PHE 0.019 0.001 PHE B 169 TRP 0.008 0.001 TRP A 776 HIS 0.020 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00265 (16123) covalent geometry : angle 0.53928 (21797) SS BOND : bond 0.00339 ( 2) SS BOND : angle 1.92094 ( 4) hydrogen bonds : bond 0.03858 ( 661) hydrogen bonds : angle 4.68153 ( 1902) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 184 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7904 (mttm) cc_final: 0.7323 (mmtt) REVERT: A 146 HIS cc_start: 0.7336 (OUTLIER) cc_final: 0.6768 (p90) REVERT: A 175 ASP cc_start: 0.6702 (p0) cc_final: 0.5924 (m-30) REVERT: A 180 ASP cc_start: 0.7672 (m-30) cc_final: 0.7445 (m-30) REVERT: A 227 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: A 266 ASP cc_start: 0.7404 (m-30) cc_final: 0.7186 (t70) REVERT: A 285 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8173 (tt) REVERT: A 288 PHE cc_start: 0.6290 (OUTLIER) cc_final: 0.5997 (p90) REVERT: A 297 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.6615 (p-80) REVERT: A 401 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8217 (mp) REVERT: A 448 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7699 (pt0) REVERT: A 458 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7603 (pm20) REVERT: A 543 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6499 (pp20) REVERT: A 575 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8164 (p0) REVERT: A 657 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7308 (mttp) REVERT: A 702 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: A 728 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7803 (tt) REVERT: A 746 GLU cc_start: 0.7820 (pt0) cc_final: 0.7423 (pt0) REVERT: A 872 LYS cc_start: 0.7299 (tptp) cc_final: 0.6783 (ttpp) REVERT: B 90 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7295 (pt) REVERT: B 205 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6854 (tp30) REVERT: B 381 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: B 407 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7102 (mp10) REVERT: B 416 ASP cc_start: 0.7695 (m-30) cc_final: 0.7448 (m-30) REVERT: B 436 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7408 (mtpp) REVERT: B 521 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6744 (pttp) REVERT: B 774 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7389 (mtt-85) REVERT: B 853 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7706 (mt-10) REVERT: B 872 LYS cc_start: 0.7534 (mttp) cc_final: 0.6811 (tmmt) REVERT: B 997 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7301 (tt0) outliers start: 60 outliers final: 23 residues processed: 228 average time/residue: 0.5975 time to fit residues: 150.5077 Evaluate side-chains 218 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 621 GLN Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 1 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: ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A 680 GLN ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.145992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126324 restraints weight = 16559.076| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.14 r_work: 0.3274 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16125 Z= 0.132 Angle : 0.562 7.046 21801 Z= 0.286 Chirality : 0.043 0.145 2345 Planarity : 0.004 0.042 2818 Dihedral : 4.430 17.933 2083 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.61 % Allowed : 18.70 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.19), residues: 1905 helix: 0.93 (0.19), residues: 797 sheet: 0.39 (0.28), residues: 365 loop : -1.26 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.018 0.001 TYR B 500 PHE 0.020 0.002 PHE B 169 TRP 0.008 0.001 TRP A 776 HIS 0.017 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00321 (16123) covalent geometry : angle 0.56161 (21797) SS BOND : bond 0.00321 ( 2) SS BOND : angle 1.84147 ( 4) hydrogen bonds : bond 0.04053 ( 661) hydrogen bonds : angle 4.66474 ( 1902) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 178 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7950 (mttm) cc_final: 0.7549 (mmtm) REVERT: A 146 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.6799 (p90) REVERT: A 180 ASP cc_start: 0.7692 (m-30) cc_final: 0.7470 (m-30) REVERT: A 227 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: A 266 ASP cc_start: 0.7398 (m-30) cc_final: 0.7189 (t70) REVERT: A 285 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8224 (tt) REVERT: A 297 HIS cc_start: 0.7300 (OUTLIER) cc_final: 0.6618 (p-80) REVERT: A 401 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8248 (mp) REVERT: A 448 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: A 458 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7658 (pm20) REVERT: A 503 GLU cc_start: 0.5230 (tt0) cc_final: 0.4433 (mm-30) REVERT: A 543 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6610 (pp20) REVERT: A 575 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8068 (p0) REVERT: A 657 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7366 (mttp) REVERT: A 702 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8179 (mp0) REVERT: A 728 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.7903 (tt) REVERT: A 746 GLU cc_start: 0.7861 (pt0) cc_final: 0.7489 (pt0) REVERT: A 872 LYS cc_start: 0.7371 (tptp) cc_final: 0.6883 (ttpp) REVERT: B 90 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7349 (pt) REVERT: B 163 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7261 (m-30) REVERT: B 205 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6892 (tp30) REVERT: B 407 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7161 (mp10) REVERT: B 416 ASP cc_start: 0.7739 (m-30) cc_final: 0.7483 (m-30) REVERT: B 436 LYS cc_start: 0.7812 (ttpp) cc_final: 0.7492 (mtpp) REVERT: B 621 GLN cc_start: 0.8704 (mt0) cc_final: 0.8213 (mp10) REVERT: B 774 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7456 (mtt-85) REVERT: B 853 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7718 (mt-10) REVERT: B 872 LYS cc_start: 0.7678 (mttp) cc_final: 0.6905 (tmmt) REVERT: B 997 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7452 (tt0) outliers start: 62 outliers final: 25 residues processed: 226 average time/residue: 0.6372 time to fit residues: 158.8594 Evaluate side-chains 215 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A 680 GLN A 796 GLN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 363 GLN ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.143096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.121508 restraints weight = 16870.423| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.29 r_work: 0.3271 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16125 Z= 0.114 Angle : 0.543 7.410 21801 Z= 0.278 Chirality : 0.043 0.146 2345 Planarity : 0.004 0.041 2818 Dihedral : 4.342 17.438 2083 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.09 % Allowed : 19.22 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.19), residues: 1905 helix: 1.09 (0.19), residues: 798 sheet: 0.36 (0.28), residues: 361 loop : -1.18 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 261 TYR 0.013 0.001 TYR B 500 PHE 0.019 0.001 PHE B 169 TRP 0.007 0.001 TRP A 776 HIS 0.017 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00268 (16123) covalent geometry : angle 0.54276 (21797) SS BOND : bond 0.00282 ( 2) SS BOND : angle 1.58906 ( 4) hydrogen bonds : bond 0.03796 ( 661) hydrogen bonds : angle 4.59836 ( 1902) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7917 (mttm) cc_final: 0.7460 (mmtm) REVERT: A 146 HIS cc_start: 0.7270 (OUTLIER) cc_final: 0.6781 (p90) REVERT: A 180 ASP cc_start: 0.7575 (m-30) cc_final: 0.7326 (m-30) REVERT: A 227 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: A 285 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8208 (tt) REVERT: A 297 HIS cc_start: 0.7022 (OUTLIER) cc_final: 0.6165 (p-80) REVERT: A 401 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8208 (mp) REVERT: A 448 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7529 (pt0) REVERT: A 458 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7864 (pm20) REVERT: A 503 GLU cc_start: 0.5193 (tt0) cc_final: 0.4417 (mm-30) REVERT: A 543 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6581 (pp20) REVERT: A 575 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8082 (p0) REVERT: A 657 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7312 (mttp) REVERT: A 702 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: A 728 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7781 (tt) REVERT: A 746 GLU cc_start: 0.7836 (pt0) cc_final: 0.7361 (pt0) REVERT: A 871 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7151 (pt0) REVERT: A 872 LYS cc_start: 0.7247 (tptp) cc_final: 0.6706 (ttpp) REVERT: B 90 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7165 (pt) REVERT: B 137 SER cc_start: 0.8406 (m) cc_final: 0.7961 (p) REVERT: B 159 GLU cc_start: 0.8045 (tp30) cc_final: 0.7355 (tt0) REVERT: B 205 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: B 407 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7113 (mp10) REVERT: B 416 ASP cc_start: 0.7670 (m-30) cc_final: 0.7427 (m-30) REVERT: B 436 LYS cc_start: 0.7806 (ttpp) cc_final: 0.7450 (mtpp) REVERT: B 521 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6659 (pttp) REVERT: B 621 GLN cc_start: 0.8727 (mt0) cc_final: 0.8281 (mp10) REVERT: B 774 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7407 (mtt-85) REVERT: B 853 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7743 (mt-10) REVERT: B 872 LYS cc_start: 0.7496 (mttp) cc_final: 0.6732 (tmmt) REVERT: B 997 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7441 (tt0) outliers start: 53 outliers final: 26 residues processed: 227 average time/residue: 0.6160 time to fit residues: 154.4241 Evaluate side-chains 221 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 162 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 161 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS A 621 GLN A 680 GLN A 787 ASN A 796 GLN A 851 GLN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120616 restraints weight = 16794.864| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.27 r_work: 0.3260 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16125 Z= 0.130 Angle : 0.566 8.733 21801 Z= 0.288 Chirality : 0.043 0.145 2345 Planarity : 0.004 0.042 2818 Dihedral : 4.370 17.067 2083 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.91 % Allowed : 19.51 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.19), residues: 1905 helix: 1.09 (0.19), residues: 799 sheet: 0.46 (0.28), residues: 358 loop : -1.19 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.019 0.001 TYR B 500 PHE 0.020 0.002 PHE B 169 TRP 0.009 0.001 TRP A 776 HIS 0.016 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00317 (16123) covalent geometry : angle 0.56583 (21797) SS BOND : bond 0.00284 ( 2) SS BOND : angle 1.59636 ( 4) hydrogen bonds : bond 0.03996 ( 661) hydrogen bonds : angle 4.60719 ( 1902) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7951 (mttm) cc_final: 0.7372 (mmtt) REVERT: A 155 HIS cc_start: 0.5709 (OUTLIER) cc_final: 0.5386 (t70) REVERT: A 180 ASP cc_start: 0.7577 (m-30) cc_final: 0.7328 (m-30) REVERT: A 227 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: A 277 GLU cc_start: 0.7474 (tt0) cc_final: 0.7232 (tt0) REVERT: A 285 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8210 (tt) REVERT: A 297 HIS cc_start: 0.6931 (OUTLIER) cc_final: 0.6093 (p-80) REVERT: A 448 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7559 (pt0) REVERT: A 458 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7848 (pm20) REVERT: A 503 GLU cc_start: 0.5111 (tt0) cc_final: 0.4409 (mm-30) REVERT: A 575 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8103 (p0) REVERT: A 657 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7330 (mttp) REVERT: A 702 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: A 728 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7866 (tt) REVERT: A 746 GLU cc_start: 0.7854 (pt0) cc_final: 0.7391 (pt0) REVERT: A 851 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: A 871 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7129 (pt0) REVERT: A 872 LYS cc_start: 0.7258 (tptp) cc_final: 0.6727 (ttpp) REVERT: B 90 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7219 (pt) REVERT: B 137 SER cc_start: 0.8467 (m) cc_final: 0.8022 (p) REVERT: B 159 GLU cc_start: 0.8040 (tp30) cc_final: 0.7349 (tt0) REVERT: B 163 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: B 407 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7123 (mp10) REVERT: B 416 ASP cc_start: 0.7682 (m-30) cc_final: 0.7434 (m-30) REVERT: B 436 LYS cc_start: 0.7892 (ttpp) cc_final: 0.7536 (mtpp) REVERT: B 521 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6648 (pttp) REVERT: B 621 GLN cc_start: 0.8695 (mt0) cc_final: 0.8335 (mp10) REVERT: B 774 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7418 (mtt-85) REVERT: B 853 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7728 (mt-10) REVERT: B 872 LYS cc_start: 0.7552 (mttp) cc_final: 0.6800 (tmmt) REVERT: B 997 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7484 (tt0) outliers start: 50 outliers final: 26 residues processed: 216 average time/residue: 0.6420 time to fit residues: 152.7651 Evaluate side-chains 219 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 621 GLN Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 851 GLN Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 163 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 95 optimal weight: 0.0020 chunk 52 optimal weight: 0.3980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS A 621 GLN A 680 GLN A 787 ASN A 796 GLN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.143087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.121619 restraints weight = 16742.799| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.28 r_work: 0.3272 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16125 Z= 0.115 Angle : 0.554 7.986 21801 Z= 0.283 Chirality : 0.042 0.148 2345 Planarity : 0.004 0.041 2818 Dihedral : 4.329 18.471 2083 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.74 % Allowed : 19.45 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.19), residues: 1905 helix: 1.18 (0.19), residues: 799 sheet: 0.41 (0.28), residues: 361 loop : -1.12 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 261 TYR 0.019 0.001 TYR B 500 PHE 0.019 0.001 PHE B 169 TRP 0.007 0.001 TRP A 776 HIS 0.030 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00263 (16123) covalent geometry : angle 0.55375 (21797) SS BOND : bond 0.00268 ( 2) SS BOND : angle 1.44697 ( 4) hydrogen bonds : bond 0.03784 ( 661) hydrogen bonds : angle 4.57707 ( 1902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5153.47 seconds wall clock time: 88 minutes 21.31 seconds (5301.31 seconds total)