Starting phenix.real_space_refine on Sat Jun 14 03:42:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rzi_24761/06_2025/7rzi_24761.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rzi_24761/06_2025/7rzi_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_24761/06_2025/7rzi_24761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rzi_24761/06_2025/7rzi_24761.map" model { file = "/net/cci-nas-00/data/ceres_data/7rzi_24761/06_2025/7rzi_24761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rzi_24761/06_2025/7rzi_24761.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.60, per 1000 atoms: 0.55 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: 3.89 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.67 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: 5.42 Time building geometry restraints manager: 4.42 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: 1.050 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: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 34.450 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.000 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.034 0.003 TRP A 695 HIS 0.017 0.002 HIS B 291 PHE 0.042 0.003 PHE A 168 TYR 0.029 0.003 TYR A 940 ARG 0.018 0.001 ARG B 261 Details of bonding type rmsd hydrogen bonds : bond 0.19937 ( 661) hydrogen bonds : angle 8.36895 ( 1902) SS BOND : bond 0.20524 ( 2) SS BOND : angle 13.13782 ( 4) covalent geometry : bond 0.00573 (16123) covalent geometry : angle 0.97152 (21797) *********************** 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 : 1.773 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: 0.7194 (tmmt) REVERT: c 5 GLN cc_start: 0.5489 (OUTLIER) cc_final: 0.4524 (mm110) outliers start: 8 outliers final: 1 residues processed: 314 average time/residue: 1.3865 time to fit residues: 476.8145 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 : 1.658 ------------------------------------------------------------------------------- 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 159 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 502 GLN A 621 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN A 957 HIS B 93 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN B 605 ASN B 677 GLN B 788 ASN B 796 GLN ** B 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** 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 = 0.3654 r_free = 0.3654 target = 0.150080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129940 restraints weight = 16984.243| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.24 r_work: 0.3372 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16125 Z= 0.138 Angle : 0.640 8.344 21801 Z= 0.329 Chirality : 0.045 0.174 2345 Planarity : 0.005 0.052 2818 Dihedral : 5.223 22.727 2088 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.26 % Allowed : 10.60 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.17), residues: 1905 helix: -1.20 (0.17), residues: 784 sheet: -1.11 (0.26), residues: 361 loop : -1.81 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 776 HIS 0.006 0.001 HIS B 291 PHE 0.023 0.002 PHE A 168 TYR 0.021 0.002 TYR B 249 ARG 0.009 0.001 ARG B 477 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 661) hydrogen bonds : angle 5.56158 ( 1902) SS BOND : bond 0.01048 ( 2) SS BOND : angle 1.75280 ( 4) covalent geometry : bond 0.00317 (16123) covalent geometry : angle 0.63936 (21797) *********************** 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 275 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 2.210 Fit side-chains revert: symmetry clash REVERT: A 146 HIS cc_start: 0.7251 (OUTLIER) cc_final: 0.5454 (p90) REVERT: A 175 ASP cc_start: 0.6744 (p0) cc_final: 0.6150 (m-30) REVERT: A 205 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6251 (mt-10) REVERT: A 448 GLU cc_start: 0.8037 (pm20) cc_final: 0.7714 (pt0) REVERT: A 792 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8548 (tm-30) REVERT: A 872 LYS cc_start: 0.7173 (tptp) cc_final: 0.6565 (ttpp) REVERT: B 61 LYS cc_start: 0.7569 (mtmm) cc_final: 0.7237 (mptt) REVERT: B 526 THR cc_start: 0.8262 (p) cc_final: 0.7905 (t) REVERT: B 774 ARG cc_start: 0.7760 (mtp85) cc_final: 0.6978 (mtt-85) REVERT: B 872 LYS cc_start: 0.7379 (mttp) cc_final: 0.6684 (tmmt) REVERT: B 997 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7139 (tt0) REVERT: B 1000 ARG cc_start: 0.7858 (ttm170) cc_final: 0.7632 (ttm170) outliers start: 56 outliers final: 15 residues processed: 258 average time/residue: 1.9099 time to fit residues: 544.1075 Evaluate side-chains 197 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 2.248 ------------------------------------------------------------------------------- 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 301 LEU Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 792 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 521 LYS 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 141 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 176 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A 680 GLN A 788 ASN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 671 ASN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 743 GLN ** B 844 GLN ** 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 = 0.3722 r_free = 0.3722 target = 0.153750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.134337 restraints weight = 16303.791| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.15 r_work: 0.3395 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16125 Z= 0.135 Angle : 0.598 7.604 21801 Z= 0.304 Chirality : 0.044 0.153 2345 Planarity : 0.004 0.048 2818 Dihedral : 4.788 21.650 2083 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.08 % Allowed : 12.81 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.18), residues: 1905 helix: -0.23 (0.18), residues: 796 sheet: -0.53 (0.27), residues: 362 loop : -1.65 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 776 HIS 0.010 0.001 HIS B 957 PHE 0.021 0.002 PHE B 169 TYR 0.018 0.002 TYR A 634 ARG 0.003 0.001 ARG A 491 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 661) hydrogen bonds : angle 4.97623 ( 1902) SS BOND : bond 0.00021 ( 2) SS BOND : angle 2.05131 ( 4) covalent geometry : bond 0.00320 (16123) covalent geometry : angle 0.59702 (21797) *********************** 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 276 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 206 time to evaluate : 2.430 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7777 (mttm) cc_final: 0.7519 (mmtt) REVERT: A 146 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.5701 (p90) REVERT: A 175 ASP cc_start: 0.6779 (p0) cc_final: 0.6360 (m-30) REVERT: A 205 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: A 448 GLU cc_start: 0.8251 (pm20) cc_final: 0.7922 (pt0) REVERT: A 500 TYR cc_start: 0.8589 (p90) cc_final: 0.8319 (p90) REVERT: A 635 ASN cc_start: 0.7517 (t0) cc_final: 0.7237 (t0) REVERT: A 699 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: A 792 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8563 (tp30) REVERT: A 872 LYS cc_start: 0.7495 (tptp) cc_final: 0.6946 (ttpp) REVERT: B 82 THR cc_start: 0.8998 (m) cc_final: 0.8540 (p) REVERT: B 500 TYR cc_start: 0.8476 (p90) cc_final: 0.8243 (p90) REVERT: B 667 MET cc_start: 0.8593 (tpp) cc_final: 0.8319 (tpt) REVERT: B 774 ARG cc_start: 0.7980 (mtp85) cc_final: 0.7379 (mtp85) REVERT: B 853 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7717 (mt-10) REVERT: B 872 LYS cc_start: 0.7589 (mttp) cc_final: 0.6948 (tmmt) REVERT: B 997 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7477 (tt0) REVERT: B 1000 ARG cc_start: 0.7995 (ttm170) cc_final: 0.7698 (mtm-85) REVERT: a 8 THR cc_start: 0.3646 (OUTLIER) cc_final: 0.3399 (m) outliers start: 70 outliers final: 27 residues processed: 258 average time/residue: 1.4909 time to fit residues: 428.8759 Evaluate side-chains 211 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 1.734 ------------------------------------------------------------------------------- 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 256 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 540 LEU 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 785 VAL 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 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 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 Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 10 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 56 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 173 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN A 915 GLN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 363 GLN B 671 ASN B 677 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.145654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126016 restraints weight = 16641.277| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.15 r_work: 0.3246 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16125 Z= 0.209 Angle : 0.688 8.202 21801 Z= 0.347 Chirality : 0.048 0.157 2345 Planarity : 0.005 0.049 2818 Dihedral : 4.958 21.411 2083 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.72 % Allowed : 14.15 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.18), residues: 1905 helix: 0.05 (0.18), residues: 793 sheet: -0.16 (0.27), residues: 365 loop : -1.63 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 776 HIS 0.015 0.002 HIS B 957 PHE 0.025 0.002 PHE B 169 TYR 0.029 0.002 TYR A 302 ARG 0.005 0.001 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.05067 ( 661) hydrogen bonds : angle 5.03774 ( 1902) SS BOND : bond 0.00041 ( 2) SS BOND : angle 2.18754 ( 4) covalent geometry : bond 0.00525 (16123) covalent geometry : angle 0.68787 (21797) *********************** 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 283 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 202 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7826 (mttm) cc_final: 0.7383 (mmtt) REVERT: A 146 HIS cc_start: 0.7585 (OUTLIER) cc_final: 0.6730 (p90) REVERT: A 175 ASP cc_start: 0.6978 (p0) cc_final: 0.5898 (m-30) REVERT: A 205 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: A 227 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: A 288 PHE cc_start: 0.6340 (OUTLIER) cc_final: 0.4838 (p90) REVERT: A 448 GLU cc_start: 0.8342 (pm20) cc_final: 0.7958 (pt0) REVERT: A 458 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7566 (pm20) REVERT: A 483 LYS cc_start: 0.8889 (mtpp) cc_final: 0.8577 (mttt) REVERT: A 699 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: A 728 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8140 (tt) REVERT: A 792 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8747 (OUTLIER) REVERT: A 799 MET cc_start: 0.8495 (mtp) cc_final: 0.8283 (mtp) REVERT: A 872 LYS cc_start: 0.7487 (tptp) cc_final: 0.6996 (ttpp) REVERT: B 90 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7451 (pt) REVERT: B 159 GLU cc_start: 0.7665 (tp30) cc_final: 0.7323 (tp30) REVERT: B 188 SER cc_start: 0.7978 (m) cc_final: 0.7280 (p) REVERT: B 205 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6893 (tp30) REVERT: B 407 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7841 (tp40) REVERT: B 436 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7389 (mtpp) REVERT: B 521 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6799 (pttp) REVERT: B 730 HIS cc_start: 0.8310 (OUTLIER) cc_final: 0.8097 (p90) REVERT: B 774 ARG cc_start: 0.7904 (mtp85) cc_final: 0.7217 (mtp85) REVERT: B 853 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7635 (mt-10) REVERT: B 872 LYS cc_start: 0.7555 (mttp) cc_final: 0.6870 (tmmt) REVERT: B 997 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7252 (tt0) outliers start: 81 outliers final: 32 residues processed: 262 average time/residue: 1.3078 time to fit residues: 378.9082 Evaluate side-chains 226 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 271 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 466 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 540 LEU 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 728 LEU Chi-restraints excluded: chain A residue 792 GLU 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 205 GLU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 VAL 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 612 GLU Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 730 HIS 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 Chi-restraints excluded: chain a residue 8 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 102 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 635 ASN A 680 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** B 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.149147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.129501 restraints weight = 16721.638| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.16 r_work: 0.3321 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3231 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= 0.120 Angle : 0.555 6.793 21801 Z= 0.285 Chirality : 0.043 0.156 2345 Planarity : 0.004 0.046 2818 Dihedral : 4.586 19.796 2083 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.79 % Allowed : 16.66 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.19), residues: 1905 helix: 0.50 (0.19), residues: 796 sheet: -0.02 (0.27), residues: 361 loop : -1.48 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 776 HIS 0.007 0.001 HIS B 957 PHE 0.018 0.001 PHE B 169 TYR 0.015 0.001 TYR A 224 ARG 0.004 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 661) hydrogen bonds : angle 4.74690 ( 1902) SS BOND : bond 0.00104 ( 2) SS BOND : angle 3.21626 ( 4) covalent geometry : bond 0.00282 (16123) covalent geometry : angle 0.55340 (21797) *********************** 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 258 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 193 time to evaluate : 1.651 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7908 (mttm) cc_final: 0.7551 (mmtm) REVERT: A 119 LYS cc_start: 0.8457 (ptpp) cc_final: 0.8202 (pttm) REVERT: A 146 HIS cc_start: 0.7358 (OUTLIER) cc_final: 0.6765 (p90) REVERT: A 175 ASP cc_start: 0.6651 (p0) cc_final: 0.5822 (m-30) REVERT: A 205 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: A 288 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.5185 (p90) REVERT: A 448 GLU cc_start: 0.8113 (pm20) cc_final: 0.7670 (pt0) REVERT: A 458 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7619 (pm20) REVERT: A 575 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8188 (p0) REVERT: A 699 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: A 702 GLU cc_start: 0.8285 (mp0) cc_final: 0.7848 (mp0) REVERT: A 728 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.7911 (tt) REVERT: A 872 LYS cc_start: 0.7421 (tptp) cc_final: 0.6917 (ttpp) REVERT: B 113 MET cc_start: 0.7785 (tpp) cc_final: 0.7461 (mmm) REVERT: B 205 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6860 (tp30) REVERT: B 436 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7438 (mtpp) REVERT: B 521 LYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6674 (pttp) REVERT: B 774 ARG cc_start: 0.7964 (mtp85) cc_final: 0.7322 (mtt-85) REVERT: B 853 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7753 (mt-10) REVERT: B 872 LYS cc_start: 0.7545 (mttp) cc_final: 0.6919 (tmmt) REVERT: B 997 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7324 (tt0) REVERT: a 8 THR cc_start: 0.4103 (OUTLIER) cc_final: 0.3782 (m) outliers start: 65 outliers final: 22 residues processed: 242 average time/residue: 1.2230 time to fit residues: 328.4638 Evaluate side-chains 210 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 1.670 ------------------------------------------------------------------------------- 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 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 401 LEU 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 699 GLU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 1009 LYS 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 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 617 SER Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain a residue 8 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 169 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.145670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124325 restraints weight = 16706.384| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.26 r_work: 0.3273 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16125 Z= 0.141 Angle : 0.582 6.754 21801 Z= 0.295 Chirality : 0.044 0.154 2345 Planarity : 0.004 0.044 2818 Dihedral : 4.528 18.884 2083 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.67 % Allowed : 17.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 1905 helix: 0.66 (0.19), residues: 798 sheet: 0.19 (0.28), residues: 366 loop : -1.42 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 776 HIS 0.009 0.001 HIS B 957 PHE 0.020 0.002 PHE B 169 TYR 0.020 0.002 TYR A 302 ARG 0.003 0.000 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 661) hydrogen bonds : angle 4.72038 ( 1902) SS BOND : bond 0.00320 ( 2) SS BOND : angle 2.65359 ( 4) covalent geometry : bond 0.00344 (16123) covalent geometry : angle 0.58054 (21797) *********************** 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 253 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 190 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7875 (mttm) cc_final: 0.7312 (mmtt) REVERT: A 146 HIS cc_start: 0.7470 (OUTLIER) cc_final: 0.6801 (p90) REVERT: A 175 ASP cc_start: 0.6661 (p0) cc_final: 0.5891 (m-30) REVERT: A 205 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: A 227 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: A 288 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.6305 (p90) REVERT: A 297 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.7011 (p-80) REVERT: A 448 GLU cc_start: 0.8124 (pm20) cc_final: 0.7797 (pt0) REVERT: A 458 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7594 (pm20) REVERT: A 543 GLU cc_start: 0.6722 (pp20) cc_final: 0.6392 (pp20) REVERT: A 575 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8121 (p0) REVERT: A 699 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8048 (mt-10) REVERT: A 702 GLU cc_start: 0.8306 (mp0) cc_final: 0.7942 (mp0) REVERT: A 728 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.7957 (tt) REVERT: A 872 LYS cc_start: 0.7350 (tptp) cc_final: 0.6843 (ttpp) REVERT: B 90 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7335 (pt) REVERT: B 163 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7266 (m-30) REVERT: B 205 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6912 (tp30) REVERT: B 436 LYS cc_start: 0.7663 (ttpp) cc_final: 0.7380 (mtpp) REVERT: B 521 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6690 (pttp) REVERT: B 774 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7359 (mtt-85) REVERT: B 853 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7756 (mt-10) REVERT: B 872 LYS cc_start: 0.7478 (mttp) cc_final: 0.6823 (tmmt) REVERT: B 997 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7357 (tt0) outliers start: 63 outliers final: 27 residues processed: 237 average time/residue: 1.2869 time to fit residues: 339.1266 Evaluate side-chains 217 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 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 699 GLU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 759 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 205 GLU Chi-restraints excluded: chain B residue 248 TYR 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 385 LEU 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 577 GLU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 12 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 172 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN 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 621 GLN ** 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 = 0.3599 r_free = 0.3599 target = 0.143556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121805 restraints weight = 16744.711| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.30 r_work: 0.3239 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16125 Z= 0.154 Angle : 0.595 6.982 21801 Z= 0.302 Chirality : 0.045 0.155 2345 Planarity : 0.004 0.044 2818 Dihedral : 4.541 18.503 2083 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.61 % Allowed : 18.11 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.19), residues: 1905 helix: 0.73 (0.19), residues: 798 sheet: 0.28 (0.28), residues: 365 loop : -1.40 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 776 HIS 0.019 0.002 HIS A 297 PHE 0.020 0.002 PHE B 169 TYR 0.019 0.002 TYR A 302 ARG 0.003 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 661) hydrogen bonds : angle 4.72734 ( 1902) SS BOND : bond 0.00360 ( 2) SS BOND : angle 2.19517 ( 4) covalent geometry : bond 0.00381 (16123) covalent geometry : angle 0.59448 (21797) *********************** 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 246 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 184 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7913 (mttm) cc_final: 0.7323 (mmtt) REVERT: A 146 HIS cc_start: 0.7509 (OUTLIER) cc_final: 0.6787 (p90) REVERT: A 175 ASP cc_start: 0.6693 (p0) cc_final: 0.5920 (m-30) REVERT: A 205 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: A 227 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: A 285 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8176 (tt) REVERT: A 288 PHE cc_start: 0.6675 (OUTLIER) cc_final: 0.6381 (p90) REVERT: A 297 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.6666 (p-80) REVERT: A 448 GLU cc_start: 0.8163 (pm20) cc_final: 0.7862 (pt0) REVERT: A 458 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7611 (pm20) REVERT: A 575 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8165 (p0) REVERT: A 632 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8620 (ptpp) REVERT: A 699 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: A 702 GLU cc_start: 0.8294 (mp0) cc_final: 0.7899 (mp0) REVERT: A 728 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.7967 (tt) REVERT: A 746 GLU cc_start: 0.7882 (pt0) cc_final: 0.7459 (pt0) REVERT: A 872 LYS cc_start: 0.7369 (tptp) cc_final: 0.6832 (ttpp) REVERT: B 90 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7400 (pt) REVERT: B 159 GLU cc_start: 0.7666 (tp30) cc_final: 0.7310 (tt0) REVERT: B 163 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: B 205 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6961 (tp30) REVERT: B 381 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: B 436 LYS cc_start: 0.7767 (ttpp) cc_final: 0.7455 (mtpp) REVERT: B 521 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6809 (pttp) REVERT: B 667 MET cc_start: 0.8652 (tpp) cc_final: 0.8393 (tpt) REVERT: B 746 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7131 (pt0) REVERT: B 774 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7327 (mtt-85) REVERT: B 853 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7777 (mt-10) REVERT: B 872 LYS cc_start: 0.7528 (mttp) cc_final: 0.6830 (tmmt) REVERT: B 994 ASN cc_start: 0.8404 (p0) cc_final: 0.7877 (p0) REVERT: B 997 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7011 (tt0) outliers start: 62 outliers final: 28 residues processed: 231 average time/residue: 1.2816 time to fit residues: 326.9344 Evaluate side-chains 216 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 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 621 GLN Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 792 GLU 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 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 498 THR Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain B residue 759 LEU 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 74 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3573 r_free = 0.3573 target = 0.141944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.120711 restraints weight = 16779.605| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.24 r_work: 0.3274 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3627 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= 0.119 Angle : 0.555 6.817 21801 Z= 0.283 Chirality : 0.043 0.169 2345 Planarity : 0.004 0.042 2818 Dihedral : 4.420 18.091 2083 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.49 % Allowed : 18.52 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 1905 helix: 0.92 (0.19), residues: 796 sheet: 0.23 (0.28), residues: 364 loop : -1.34 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 776 HIS 0.016 0.001 HIS A 297 PHE 0.019 0.001 PHE B 169 TYR 0.017 0.001 TYR B 500 ARG 0.002 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 661) hydrogen bonds : angle 4.65124 ( 1902) SS BOND : bond 0.00276 ( 2) SS BOND : angle 1.76869 ( 4) covalent geometry : bond 0.00281 (16123) covalent geometry : angle 0.55433 (21797) *********************** 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: 60 poor density : 180 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7926 (mttm) cc_final: 0.7356 (mmtt) REVERT: A 146 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.6758 (p90) REVERT: A 175 ASP cc_start: 0.6615 (p0) cc_final: 0.5973 (m-30) REVERT: A 205 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: A 285 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8202 (tt) REVERT: A 288 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.6412 (p90) REVERT: A 297 HIS cc_start: 0.7197 (OUTLIER) cc_final: 0.6510 (p-80) REVERT: A 448 GLU cc_start: 0.8069 (pm20) cc_final: 0.7753 (pt0) REVERT: A 458 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7621 (pm20) REVERT: A 543 GLU cc_start: 0.6909 (pp20) cc_final: 0.6669 (pp20) REVERT: A 575 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8093 (p0) REVERT: A 632 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8600 (ptpp) REVERT: A 702 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: A 728 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.7832 (tt) REVERT: A 746 GLU cc_start: 0.7819 (pt0) cc_final: 0.7434 (pt0) REVERT: A 872 LYS cc_start: 0.7314 (tptp) cc_final: 0.6790 (ttpp) REVERT: A 910 GLU cc_start: 0.7702 (pt0) cc_final: 0.7493 (pt0) REVERT: B 90 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7322 (pt) REVERT: B 163 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: B 205 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6921 (tp30) REVERT: B 381 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: B 436 LYS cc_start: 0.7755 (ttpp) cc_final: 0.7432 (mtpp) REVERT: B 521 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6723 (pttp) REVERT: B 621 GLN cc_start: 0.8739 (mt0) cc_final: 0.8251 (mp10) REVERT: B 702 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7127 (tp30) REVERT: B 774 ARG cc_start: 0.7951 (mtp85) cc_final: 0.7330 (mtt-85) REVERT: B 853 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7728 (mt-10) REVERT: B 872 LYS cc_start: 0.7522 (mttp) cc_final: 0.6803 (tmmt) REVERT: B 997 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7358 (tt0) outliers start: 60 outliers final: 25 residues processed: 225 average time/residue: 1.3112 time to fit residues: 325.3660 Evaluate side-chains 222 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 1.653 ------------------------------------------------------------------------------- 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 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 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 632 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 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 381 GLU Chi-restraints excluded: chain B residue 385 LEU 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 577 GLU Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain a residue 8 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 72 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 156 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 0.0870 chunk 86 optimal weight: 2.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN A 621 GLN A 680 GLN A 788 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 ASN B 407 GLN ** 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 = 0.3618 r_free = 0.3618 target = 0.145459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.123775 restraints weight = 16685.757| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.31 r_work: 0.3274 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16125 Z= 0.106 Angle : 0.532 6.198 21801 Z= 0.272 Chirality : 0.042 0.162 2345 Planarity : 0.004 0.041 2818 Dihedral : 4.292 17.415 2083 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.26 % Allowed : 18.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.19), residues: 1905 helix: 1.08 (0.19), residues: 799 sheet: 0.30 (0.28), residues: 361 loop : -1.24 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 776 HIS 0.016 0.001 HIS A 297 PHE 0.018 0.001 PHE B 169 TYR 0.017 0.001 TYR B 500 ARG 0.002 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 661) hydrogen bonds : angle 4.56039 ( 1902) SS BOND : bond 0.00226 ( 2) SS BOND : angle 1.49599 ( 4) covalent geometry : bond 0.00243 (16123) covalent geometry : angle 0.53127 (21797) *********************** 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 239 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7938 (mttm) cc_final: 0.7384 (mmtt) REVERT: A 146 HIS cc_start: 0.7248 (OUTLIER) cc_final: 0.6802 (p90) REVERT: A 175 ASP cc_start: 0.6477 (p0) cc_final: 0.6020 (m-30) REVERT: A 205 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6658 (mp0) REVERT: A 285 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8224 (tt) REVERT: A 288 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.6300 (p90) REVERT: A 297 HIS cc_start: 0.6946 (OUTLIER) cc_final: 0.6206 (p-80) REVERT: A 401 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8156 (mp) REVERT: A 448 GLU cc_start: 0.7947 (pm20) cc_final: 0.7463 (pt0) REVERT: A 458 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7600 (pm20) REVERT: A 460 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8463 (mtm110) REVERT: A 503 GLU cc_start: 0.5209 (tt0) cc_final: 0.4431 (mm-30) REVERT: A 543 GLU cc_start: 0.6891 (pp20) cc_final: 0.6598 (pp20) REVERT: A 575 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8127 (p0) REVERT: A 702 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: A 728 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7723 (tt) REVERT: A 746 GLU cc_start: 0.7793 (pt0) cc_final: 0.7310 (pt0) REVERT: A 872 LYS cc_start: 0.7247 (tptp) cc_final: 0.6696 (ttpp) REVERT: B 90 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7187 (pt) REVERT: B 163 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7258 (m-30) REVERT: B 436 LYS cc_start: 0.7849 (ttpp) cc_final: 0.7504 (mtpp) REVERT: B 521 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6617 (pttp) REVERT: B 621 GLN cc_start: 0.8756 (mt0) cc_final: 0.8329 (mp10) REVERT: B 702 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7153 (tp30) REVERT: B 774 ARG cc_start: 0.7943 (mtp85) cc_final: 0.7316 (mtt-85) REVERT: B 853 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7743 (mt-10) REVERT: B 872 LYS cc_start: 0.7496 (mttp) cc_final: 0.6786 (tmmt) REVERT: B 997 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7356 (tt0) outliers start: 56 outliers final: 21 residues processed: 226 average time/residue: 1.3594 time to fit residues: 342.4577 Evaluate side-chains 209 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 1.811 ------------------------------------------------------------------------------- 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 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 401 LEU Chi-restraints excluded: chain A residue 460 ARG 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 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 163 ASP 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 498 THR Chi-restraints excluded: chain B residue 517 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 702 GLU Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain a residue 8 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 86 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS A 621 GLN A 680 GLN A 788 ASN ** B 155 HIS ** 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 = 0.3586 r_free = 0.3586 target = 0.142857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.121348 restraints weight = 16959.104| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.29 r_work: 0.3269 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3753 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= 0.127 Angle : 0.567 8.340 21801 Z= 0.288 Chirality : 0.044 0.183 2345 Planarity : 0.004 0.042 2818 Dihedral : 4.322 16.980 2083 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.68 % Allowed : 19.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.19), residues: 1905 helix: 1.10 (0.19), residues: 799 sheet: 0.33 (0.28), residues: 361 loop : -1.22 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 776 HIS 0.017 0.001 HIS A 297 PHE 0.019 0.002 PHE B 169 TYR 0.020 0.001 TYR B 500 ARG 0.002 0.000 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 661) hydrogen bonds : angle 4.56800 ( 1902) SS BOND : bond 0.00248 ( 2) SS BOND : angle 1.53972 ( 4) covalent geometry : bond 0.00307 (16123) covalent geometry : angle 0.56649 (21797) ********************** 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 217 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7908 (mttm) cc_final: 0.7367 (mmtt) REVERT: A 175 ASP cc_start: 0.6489 (p0) cc_final: 0.6076 (m-30) REVERT: A 205 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: A 288 PHE cc_start: 0.6559 (OUTLIER) cc_final: 0.6260 (p90) REVERT: A 297 HIS cc_start: 0.6913 (OUTLIER) cc_final: 0.6152 (p-80) REVERT: A 401 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8166 (mp) REVERT: A 448 GLU cc_start: 0.7957 (pm20) cc_final: 0.7646 (pt0) REVERT: A 458 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7603 (pm20) REVERT: A 503 GLU cc_start: 0.5226 (tt0) cc_final: 0.4454 (mm-30) REVERT: A 575 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8109 (p0) REVERT: A 702 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: A 728 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7807 (tt) REVERT: A 746 GLU cc_start: 0.7815 (pt0) cc_final: 0.7340 (pt0) REVERT: A 787 ASN cc_start: 0.8637 (t0) cc_final: 0.8384 (t0) REVERT: A 872 LYS cc_start: 0.7281 (tptp) cc_final: 0.6731 (ttpp) REVERT: B 90 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7226 (pt) REVERT: B 163 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7235 (m-30) REVERT: B 436 LYS cc_start: 0.7864 (ttpp) cc_final: 0.7515 (mtpp) REVERT: B 521 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6662 (pttp) REVERT: B 621 GLN cc_start: 0.8771 (mt0) cc_final: 0.8407 (mp10) REVERT: B 702 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7148 (tp30) REVERT: B 774 ARG cc_start: 0.7942 (mtp85) cc_final: 0.7311 (mtt-85) REVERT: B 853 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7737 (mt-10) REVERT: B 872 LYS cc_start: 0.7602 (mttp) cc_final: 0.6859 (tmmt) REVERT: B 997 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7450 (tt0) outliers start: 46 outliers final: 23 residues processed: 207 average time/residue: 1.3011 time to fit residues: 298.0148 Evaluate side-chains 205 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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 256 VAL Chi-restraints excluded: chain A residue 278 VAL 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 401 LEU 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 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 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 498 THR Chi-restraints excluded: chain B residue 517 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 702 GLU Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain a residue 8 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.4166 > 50: distance: 9 - 14: 20.512 distance: 14 - 15: 8.752 distance: 15 - 16: 43.039 distance: 15 - 18: 25.365 distance: 16 - 17: 24.708 distance: 16 - 23: 44.917 distance: 18 - 19: 32.878 distance: 19 - 20: 9.001 distance: 20 - 21: 31.255 distance: 21 - 22: 23.201 distance: 23 - 24: 13.428 distance: 24 - 25: 12.668 distance: 24 - 27: 21.104 distance: 25 - 26: 52.870 distance: 25 - 29: 33.228 distance: 27 - 28: 32.285 distance: 29 - 30: 34.424 distance: 29 - 35: 21.919 distance: 30 - 31: 45.613 distance: 30 - 33: 34.568 distance: 31 - 32: 40.804 distance: 31 - 36: 19.355 distance: 33 - 34: 36.869 distance: 34 - 35: 23.480 distance: 36 - 37: 21.682 distance: 37 - 38: 15.826 distance: 37 - 40: 3.282 distance: 38 - 39: 38.501 distance: 38 - 45: 13.781 distance: 40 - 41: 18.808 distance: 41 - 42: 13.385 distance: 42 - 43: 12.748 distance: 42 - 44: 15.681 distance: 45 - 46: 29.028 distance: 46 - 47: 20.202 distance: 46 - 49: 33.882 distance: 47 - 48: 13.955 distance: 47 - 53: 26.934 distance: 49 - 50: 15.039 distance: 50 - 51: 15.992 distance: 50 - 52: 36.765 distance: 53 - 54: 25.540 distance: 54 - 55: 53.079 distance: 54 - 57: 41.834 distance: 55 - 56: 49.871 distance: 55 - 62: 33.146 distance: 57 - 58: 15.048 distance: 58 - 59: 30.740 distance: 59 - 60: 42.993 distance: 60 - 61: 19.900 distance: 62 - 63: 19.961 distance: 63 - 64: 29.819 distance: 63 - 66: 14.038 distance: 64 - 65: 25.184 distance: 64 - 73: 24.867 distance: 66 - 67: 19.330 distance: 67 - 68: 4.791 distance: 68 - 69: 4.150 distance: 69 - 70: 5.545 distance: 70 - 71: 8.941 distance: 70 - 72: 7.663 distance: 73 - 74: 13.982 distance: 74 - 75: 11.007 distance: 74 - 77: 17.824 distance: 75 - 76: 7.835 distance: 75 - 82: 8.129 distance: 76 - 136: 20.011 distance: 77 - 78: 21.942 distance: 78 - 79: 18.166 distance: 79 - 80: 16.539 distance: 79 - 81: 4.552 distance: 82 - 83: 6.892 distance: 83 - 84: 6.755 distance: 83 - 86: 7.692 distance: 84 - 85: 4.357 distance: 84 - 94: 9.967 distance: 86 - 87: 3.922 distance: 87 - 88: 4.149 distance: 87 - 89: 6.176 distance: 88 - 90: 3.894 distance: 89 - 91: 5.469 distance: 90 - 92: 4.296 distance: 91 - 92: 6.681 distance: 92 - 93: 3.748 distance: 94 - 95: 5.827 distance: 94 - 124: 11.136 distance: 95 - 96: 8.796 distance: 95 - 98: 4.387 distance: 96 - 97: 9.372 distance: 96 - 105: 3.779 distance: 97 - 121: 12.393 distance: 98 - 99: 7.228 distance: 101 - 102: 3.210